Proteins (Scientific journal)

published in (P1433)

Q68704269	"Dry" enzymes
Q27732118	"Ensemble" iterative relaxation matrix approach: a new NMR refinement protocol applied to the solution structure of crambin
Q27639586	1.3-A resolution structure of human glutathione S-transferase with S-hexyl glutathione bound reveals possible extended ligandin binding site
Q27684388	1.37 Å Crystal structure of pathogenic factor pectate lyase from Acidovorax citrulli
Q27730927	1.56 A structure of mature truncated human fibroblast collagenase
Q27652308	1.59 A structure of trypsin at 120 K: comparison of low temperature and room temperature structures
Q34420170	1.6 A crystal structure of YteR protein from Bacillus subtilis, a predicted lyase.
Q37471224	1.6 A crystal structure of a PA2721 protein from pseudomonas aeruginosa--a potential drug-resistance protein
Q33210883	1.70 A X-ray structure of human apo kallikrein 1: structural changes upon peptide inhibitor/substrate binding
Q27629375	1.9 A x-ray study shows closed flap conformation in crystals of tethered HIV-1 PR
Q58293616	1996 Johns Hopkins protein folding meeting
Q47625135	1H NMR structure of an antifungal gamma-thionin protein SIalpha1: similarity to scorpion toxins
Q31162716	2-5A induces a conformational change in the ankyrin-repeat domain of RNase L.
Q30424940	2.0 A resolution structure of a ternary complex of pig muscle phosphoglycerate kinase containing 3-phospho-D-glycerate and the nucleotide Mn adenylylimidodiphosphate
Q27631041	2.8-A crystal structure of a nontoxic type-II ribosome-inactivating protein, ebulin l
Q46604655	3',5' Cyclic nucleotide phosphodiesterases class III: members, structure, and catalytic mechanism
Q44525139	3(10)-helices in proteins are parahelices
Q58038984	3D domain-swapped human cystatin C with amyloidlike intermolecular β-sheets
Q31004521	3D structural model of the G‐protein‐coupled cannabinoid CB2 receptor
Q33573786	3DM: systematic analysis of heterogeneous superfamily data to discover protein functionalities.
Q79210028	3DS3 and 3DS5 3D-SHOTGUN meta-predictors in CAFASP3
Q30420710	3Drefine: consistent protein structure refinement by optimizing hydrogen bonding network and atomic-level energy minimization
Q73271596	3D‐SHOTGUN: A novel, cooperative, fold‐recognition meta‐predictor
Q30374011	3d interaction homology: The structurally known rotamers of tyrosine derive from a surprisingly limited set of information-rich hydropathic interaction environments described by maps.
Q130681474	AlphaFold2‐guided description of CoBaHMA, a novel family of bacterial domains within the heavy‐metal‐associated superfamily
Q53560178	A "moving metal mechanism" for substrate cleavage by the DNA repair endonuclease APE-1.
Q33210885	A "solvated rotamer" approach to modeling water-mediated hydrogen bonds at protein-protein interfaces
Q27644504	A 1.55 A resolution X-ray crystal structure of HEF2/ERH and insights into its transcriptional and cell-cycle interaction networks
Q67777633	A 175-psec molecular dynamics simulation of camphor-bound cytochrome P-450cam
Q30396558	A 3D building blocks approach to analyzing and predicting structure of proteins
Q40553690	A ?FRankenstein's monster? approach to comparative modeling: Merging the finest fragments of Fold-Recognition models and iterative model refinement aided by 3D structure evaluation
Q47282702	A Computational Method for the Design of Nested Proteins by Loop-Directed Domain Insertion.
Q47896135	A Markov-chain model description of binding funnels to enhance the ranking of docked solutions
Q81505333	A Mg2+-induced conformational switch rendering a competent DNA polymerase catalytic complex
Q54623267	A P-loop-like motif in a widespread ATP pyrophosphatase domain: implications for the evolution of sequence motifs and enzyme activity.
Q94950193	A Protein Sequence Fitness Function for Identifying Natural and Non-Natural Proteins
Q59464008	A QM/MM study of proton transport pathways in a [NiFe] hydrogenase
Q46345706	A QM/MM study of the catalytic mechanism of SAM methyltransferase RlmN from Escherichia coli.
Q53032524	A QM/MM study of the reaction mechanism of (R)-hydroxynitrile lyases from Arabidopsis thaliana (AtHNL).
Q52005742	A Shannon entropy-based filter detects high- quality profile-profile alignments in searches for remote homologues
Q79303649	A ToxR-based dominant-negative system to investigate heterotypic transmembrane domain interactions
Q30388027	A benchmark testing ground for integrating homology modeling and protein docking
Q90563024	A benchmarking study on virtual ligand screening against homology models of human GPCRs
Q30429145	A beta-complex statistical four body contact potential combined with a hydrogen bond statistical potential recognizes the correct native structure from protein decoy sets.
Q41867652	A binding free energy decomposition approach for accurate calculations of the fidelity of DNA polymerases
Q30414103	A broad specificity nucleoside kinase from Thermoplasma acidophilum
Q52388559	A calculation strategy for the structure determination of symmetric dimers by 1H NMR.
Q81494743	A chemogenomic analysis of the transmembrane binding cavity of human G-protein-coupled receptors
Q51905670	A chirality index for investigating protein secondary structures and their time evolution
Q43900308	A clade of trypsins found in cold-adapted fish
Q42084202	A coarse-grained alpha-carbon protein model with anisotropic hydrogen-bonding.
Q42662065	A coarse-grained potential for fold recognition and molecular dynamics simulations of proteins
Q51911563	A coarse-grained protein force field for folding and structure prediction.
Q41468197	A combination of rescoring and refinement significantly improves protein docking performance
Q32167461	A combinatorial library for the binuclear metal center of bacterial phosphotriesterase
Q33238967	A combinatorial score to distinguish biological and nonbiological protein-protein interfaces
Q48048981	A combinatorial scoring function for protein-RNA docking
Q46823192	A combined approach of mass spectrometry, molecular modeling, and site-directed mutagenesis highlights key structural features responsible for the thermostability of Sulfolobus solfataricus carboxypeptidase
Q43875748	A common structural scaffold in CTD phosphatases that supports distinct catalytic mechanisms.
Q37399880	A comparative analysis of the equilibrium dynamics of a designed protein inferred from NMR, X-ray, and computations
Q43022305	A comparative infrared spectroscopic study of glycoside hydrolases from extremophilic archaea revealed different molecular mechanisms of adaptation to high temperatures
Q27627415	A comparative structural analysis of the ADF/cofilin family
Q44686524	A comparative study of dynamic structures between phage 434 Cro and repressor proteins by normal mode analysis
Q47427892	A comparative study of viral capsids and bacterial compartments reveals an enriched understanding of shell dynamics.
Q57064940	A comparison of SCOP and CATH with respect to domain-domain interactions
Q45786244	A comparison of the dynamics of pantothenate synthetase from M. tuberculosis and E. coli: Computational studies
Q72868496	A comparison of the immunogenicity of a pair of enantiomeric proteins
Q58008737	A comparison of15N NMR relaxation measurements with a molecular dynamics simulation: Backbone dynamics of the glucocorticoid receptor DNA-binding domain
Q33295506	A complete library of amino acid alterations at R306 in Streptomyces clavuligerus deacetoxycephalosporin C synthase demonstrates its structural role in the ring-expansion activity
Q58484085	A complete relaxation matrix refinement of the solution structure of a paramagnetic metalloprotein: Reduced HiPIP I from Ectothiorhodospira halophila
Q36821377	A complete relaxation matrix refinement of the solution structure of a paramagnetic metalloprotein: reduced HiPIP I from Ectothiorhodospira halophila
Q30381428	A composite approach towards a complete model of the myosin rod
Q30168943	A comprehensive analysis of the Greek key motifs in protein beta-barrels and beta-sandwiches
Q34721619	A comprehensive examination of the contributions to the binding entropy of protein-ligand complexes
Q34120063	A comprehensive library of blocked dipeptides reveals intrinsic backbone conformational propensities of unfolded proteins
Q51629866	A computational analysis of the binding affinities of FKBP12 inhibitors using the MM-PB/SA method
Q51276071	A computational approach for studying antibody-antigen interactions without prior structural information: the anti-testosterone binding antibody as a case study
Q82354600	A computational investigation on the role of glycosylation in the binding of alpha1 nicotinic acetylcholine receptor with two alpha-neurotoxins
Q46274599	A computational method for selecting short peptide sequences for inorganic material binding.
Q90556723	A computational model for controlling conformational cooperativity and function in proteins
Q28295072	A computational model of the inhibition of Mycobacterium tuberculosis ATPase by a new drug candidate R207910
Q51960090	A computational protocol to probe the role of solvation effects on the reduction potential of azurin mutants
Q34372655	A computational tool for identifying minimotifs in protein–protein interactions and improving the accuracy of minimotif predictions
Q72589777	A computer model of the interleukin-4/receptor complex
Q30377365	A computer model to dynamically simulate protein folding: studies with crambin.
Q72367442	A connected-cluster of hydration around myoglobin: correlation between molecular dynamics simulations and experiment
Q30157950	A consensus algorithm to screen genomes for novel families of transmembrane beta barrel proteins
Q30193549	A consensus prediction of the secondary structure for the 6-phospho-beta-D-galactosidase superfamily
Q44515173	A consensus-binding structure for adenine at the atomic level permits searching for the ligand site in a wide spectrum of adenine-containing complexes
Q74308441	A conserved helix-unfolding motif in the naturally unfolded proteins
Q46022933	A conserved hypothetical protein from Mycoplasma genitalium shows structural homology to nusb proteins.
Q81686176	A consistent set of statistical potentials for quantifying local side-chain and backbone interactions
Q40978107	A continuum theory for the prediction of lateral and rotational positioning of alpha-helices in membrane proteins: bacteriorhodopsin.
Q51956381	A correlation-based method for the enhancement of scoring functions on funnel-shaped energy landscapes
Q27649633	A covalent S-F heterodimer of leucotoxin reveals molecular plasticity of beta-barrel pore-forming toxins
Q43900312	A critical analysis of continuum electrostatics: the screened Coulomb potential--implicit solvent model and the study of the alanine dipeptide and discrimination of misfolded structures of proteins
Q71267484	A critical assessment of comparative molecular modeling of tertiary structures of proteins
Q46415727	A critical survey of average distances between catalytic carboxyl groups in glycoside hydrolases.
Q90733842	A crystal structure of the human protein kinase Mps1 reveals an ordered conformation of the activation loop
Q30832957	A data-driven approach to modeling the tripartite structure of multidrug resistance efflux pumps.
Q56611946	A database method for automated map interpretation in protein crystallography
Q30322867	A database method for automated map interpretation in protein crystallography.
Q38561234	A database of mutants and effects of site-directed mutagenesis experiments on G protein-coupled receptors
Q91793567	A deep dense inception network for protein beta-turn prediction
Q27656745	A designed chimeric cyanovirin-N homolog lectin: Structure and molecular basis of sucrose binding
Q47307422	A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance
Q43460369	A detailed representation of electrostatic energy in prediction of sequence and pH dependence of protein stability
Q45198410	A detailed unfolding pathway of a (beta/alpha)8-barrel protein as studied by molecular dynamics simulations.
Q34468854	A differential association of Apolipoprotein E isoforms with the amyloid-β oligomer in solution.
Q45402219	A discriminative approach for identifying domain-domain interactions from protein-protein interactions
Q44419055	A distance-dependent atomic knowledge-based potential and force for discrimination of native structures from decoys
Q30328397	A distance-dependent atomic knowledge-based potential for improved protein structure selection.
Q112578723	A distinct ssDNA/RNA binding interface in the Nsp9 protein from SARS-CoV-2
Q73083588	A disulfide bridge near the active site of carbapenem-hydrolyzing class A beta-lactamases might explain their unusual substrate profile
Q81349949	A diverse view of protein dynamics from NMR studies of HIV-1 protease flaps
Q42426826	A divide‐and‐conquer approach to determine the Pareto frontier for optimization of protein engineering experiments
Q41432614	A domain of the Klenow fragment of Escherichia coli DNA polymerase I has polymerase but no exonuclease activity.
Q27655365	A dramatic conformational rearrangement is necessary for the activation of DNR from Pseudomonas aeruginosa. Crystal structure of wild-type DNR
Q46863948	A dynamic N-capping motif in cytochrome b5: evidence for a pH-controlled conformational switch
Q47925496	A dynamic model for processive transcription elongation and backtracking long pauses by multisubunit RNA polymerases
Q54336657	A dynamic model of long-range conformational adaptations triggered by nucleotide binding in GroEL-GroES.
Q36301863	A family 13 thioesterase isolated from an activated sludge metagenome: Insights into aromatic compounds metabolism.
Q42658621	A family of proteins related to Spätzle, the toll receptor ligand, are encoded in the Drosophila genome.
Q41675256	A fast algorithm for genome-wide analysis of proteins with repeated sequences.
Q52206936	A fast and simple method to calculate protonation states in proteins
Q86425594	A fast approximate method of identifying paths of allosteric communication in proteins
Q52080528	A fast method to sample real protein conformational space
Q51906613	A filter enhanced sampling and combinatorial scoring study for protein docking in CAPRI.
Q48376963	A finite element framework for computation of protein normal modes and mechanical response
Q46873034	A folding inhibitor of the HIV-1 protease.
Q46781117	A fourth generation synchrotron at SLAC?
Q91793624	A free-energy landscape for the glucagon-like peptide 1 receptor GLP1R
Q92174538	A further leap of improvement in tertiary structure prediction in CASP13 prompts new routes for future assessments
Q74419054	A fusion protein between serum amyloid A and staphylococcal nuclease—synthesis, purification, and structural studies
Q40168256	A general approach for developing system-specific functions to score protein-ligand docked complexes using support vector inductive logic programming.
Q47596362	A general clustering approach with application to the Miyazawa-Jernigan potentials for amino acids
Q52901657	A general method of domain closure is applied to phosphoglycerate kinase and the result compared with the crystal structure of a closed conformation of the enzyme
Q46698321	A generalized affine gap model significantly improves protein sequence alignment accuracy
Q34188720	A generalized approach to sampling backbone conformations with RosettaDock for CAPRI rounds 13-19
Q41381019	A generalized knowledge-based discriminatory function for biomolecular interactions
Q54252468	A genetic and physical study of the interdomain linker of E. Coli AraC protein--a trans-subunit communication pathway
Q54338499	A genetic screen to identify variants of bovine pancreatic trypsin inhibitor with altered folding energetics
Q27674956	A genetically encoded, high-signal-to-noise maltose sensor
Q56558814	A genomic perspective of protein kinases in Plasmodium falciparum
Q52401572	A geometrical constraint approach for reproducing the native backbone conformation of a protein
Q30355895	A global machine learning based scoring function for protein structure prediction.
Q51633101	A graph spectral analysis of the structural similarity network of protein chains
Q39221322	A guide to the effects of a large portion of the residues of triosephosphate isomerase on catalysis, stability, druggability, and human disease.
Q30195945	A helix-turn-strand structural motif common in α-β proteins
Q46597277	A hidden aggregation-prone structure in the heart of hypoxia inducible factor prolyl hydroxylase
Q29615859	A hierarchical approach to all-atom protein loop prediction
Q52229481	A hierarchical method for generating low-energy conformers of a protein-ligand complex
Q84898779	A hierarchical order within protein structures underlies large separations between strands in β‐sheets
Q79184855	A hinge of the endogeneous ATP synthase inhibitor protein: the link between inhibitory and anchoring domains
Q51906611	A holistic approach to protein docking
Q53942033	A homology model for the human theta-class glutathione transferase T1-1.
Q72589787	A homology model of human interferon alpha-2
Q37334362	A hybrid NMR/SAXS-based approach for discriminating oligomeric protein interfaces using Rosetta
Q43787251	A hybrid sequence approach to the paracelsus challenge
Q69444356	A hydrophobic cluster forms early in the folding of dihydrofolate reductase
Q90267408	A hyperthermophilic protein G variant engineered via directed evolution prevents the formation of toxic SOD1 oligomers
Q54567778	A hypothetical complex between crystalline flavocytochrome b2 and cytochrome c.
Q77751659	A kinetic model for the internal motions of proteins: diffusion between multiple harmonic wells
Q50899108	A knowledge-based forcefield for protein-protein interface design
Q51927664	A knowledge-based move set for protein folding
Q52026759	A knowledge-based scale for amino acid membrane propensity
Q30362842	A large data set comparison of protein structures determined by crystallography and NMR: statistical test for structural differences and the effect of crystal packing.
Q30424383	A large-scale experiment to assess protein structure prediction methods.
Q44544340	A left-handed alpha-helix containing both L- and D-amino acids: the solution structure of the antimicrobial lipodepsipeptide tolaasin
Q35963380	A less-biased analysis of metalloproteins reveals novel zinc coordination geometries
Q71763575	A lipoamide dehydrogenase from Neisseria meningitidis has a lipoyl domain
Q39115927	A machine learning approach for ranking clusters of docked protein-protein complexes by pairwise cluster comparison
Q42143961	A machine learning approach for the prediction of protein surface loop flexibility
Q45789918	A mathematically related singularity and the maximum size of protein domains.
Q30795000	A measure of progress in fold recognition?
Q42699474	A mechanism by which binding of the broadly neutralizing antibody b12 unfolds the inner domain α1 helix in an engineered HIV-1 gp120.
Q27658901	A metal-mediated hydride shift mechanism for xylose isomerase based on the 1.6 A Streptomyces rubiginosus structures with xylitol and D-xylose
Q52380142	A method for alpha-helical integral membrane protein fold prediction
Q71774368	A method for detecting hydrophobic patches on protein surfaces
Q30334411	A method for determining the positions of polar hydrogens added to a protein structure that maximizes protein hydrogen bonding
Q47604846	A method for localizing ligand binding pockets in protein structures
Q58882294	A method for partitioning the information contained in a protein sequence between its structure and function
Q33978603	A method for simultaneous alignment of multiple protein structures
Q46167114	A method for the analysis of domain movements in large biomolecular complexes
Q46754427	A method for the improvement of threading-based protein models
Q46425803	A method for the prediction of surface "U"-turns and transglobular connections in small proteins
Q52387751	A method to recognize distant repeats in protein sequences
Q41463219	A method using active-site sequence conservation to find functional shifts in protein families: application to the enzymes of central metabolism, leading to the identification of an anomalous isocitrate dehydrogenase in pathogens
Q30400559	A miniaturized technique for assessing protein thermodynamics and function using fast determination of quantitative cysteine reactivity
Q31107925	A minimalist approach to fragment-based ligand design using common rings and linkers: application to kinase inhibitors
Q35093751	A missense mutation in CLIC2 associated with intellectual disability is predicted by in silico modeling to affect protein stability and dynamics
Q51559851	A mixed molecular modeling‐robotics approach to investigate lipase large molecular motions
Q42625265	A model for human cardiac troponin C and for modulation of its Ca2+ affinity by drugs
Q72321038	A model for the LexA repressor DNA complex
Q80809756	A model for the assembly of nicotinic receptors based on subunit-subunit interactions
Q42999033	A model for the hepatitis C virus envelope glycoprotein E2.
Q30157232	A model for the interaction between NF-kappa-B and ASPP2 suggests an I-kappa-B-like binding mechanism
Q52246770	A model for the nucleotide-binding domains of ABC transporters based on the large domain of aspartate aminotransferase
Q52538859	A model for the structure of a homodimeric prohormone: the precursor to the locust neuropeptide AKH I.
Q27737034	A model of insulin fibrils derived from the x-ray crystal structure of a monomeric insulin (despentapeptide insulin)
Q30355469	A model of local-minima distribution on conformational space and its application to protein structure prediction.
Q31108068	A model of restriction endonuclease MvaI in complex with DNA: a template for interpretation of experimental data and a guide for specificity engineering
Q72303904	A model of the complex between interleukin-4 and its receptors
Q42626699	A model of the complex between the PfEMP1 malaria protein and the human ICAM-1 receptor
Q38325515	A model of the platelet factor 4 complex with heparin
Q80752697	A model study of protein nascent chain and cotranslational folding using hydrophobic-polar residues
Q56994722	A model-based proposal for the role of UreF as a GTPase-activating protein in the urease active site biosynthesis
Q30312625	A modified definition of Sov, a segment-based measure for protein secondary structure prediction assessment.
Q69761715	A molecular dynamics analysis of protein structural elements
Q30421076	A molecular dynamics approach for the generation of complete protein structures from limited coordinate data.
Q45361266	A molecular dynamics approach to study the importance of solvent in protein interactions
Q36885859	A molecular dynamics simulation study of segment B1 of protein G
Q80595817	A molecular dynamics study comparing a wild-type with a multiple drug resistant HIV protease: differences in flap and aspartate 25 cavity dimensions
Q47925571	A molecular dynamics study of C1r and C1s dimers: implications for the structure of the C1 complex.
Q54655137	A molecular dynamics study of solvent behavior around a protein.
Q51300908	A molecular dynamics study of the binary complexes of APP, JIP1, and the cargo binding domain of KLC.
Q34013248	A molecular dynamics study of the early stages of amyloid-beta(1-42) oligomerization: the role of lipid membranes
Q45161839	A molecular dynamics study of the structural stability of HIV-1 protease under physiological conditions: the role of Na+ ions in stabilizing the active site
Q30577364	A molten globule intermediate of the von Willebrand factor A1 domain firmly tethers platelets under shear flow
Q53021773	A monoclonal antibody fab fragment crystallized with and without a peptide epitope from HIV
Q27679324	A multi-faceted analysis of RutD reveals a novel family of α/β hydrolases
Q51434391	A multi-resolution model to capture both global fluctuations of an enzyme and molecular recognition in the ligand-binding site
Q81424625	A multibody, whole-residue potential for protein structures, with testing by Monte Carlo simulated annealing
Q36871044	A multicopy modeling of the water distribution in macromolecular crystals
Q30408135	A multilayer evaluation approach for protein structure prediction and model quality assessment
Q44677796	A multiple-start Monte Carlo docking method.
Q34975436	A multiple‐template approach to protein threading
Q51072404	A multiscale approach to predicting affinity changes in protein-protein interfaces.
Q40849232	A multiscale approach to simulating the conformational properties of unbound multi-C₂H₂ zinc finger proteins
Q51082035	A multiscale model for simulating binding kinetics of proteins with flexible linkers
Q68754537	A mutant T4 lysozyme (Val 131----Ala) designed to increase thermostability by the reduction of strain within an alpha-helix
Q28743851	A natural and readily available crowding agent: NMR studies of proteins in hen egg white
Q44035979	A network of dynamically conserved residues deciphers the motions of maltose transporter
Q40606078	A neural network approach to evaluate fold recognition results.
Q52221395	A new Hybrid Monte Carlo algorithm for protein potential function test and structure refinement
Q54341267	A new and unexpected domain-domain interaction in the AraC protein
Q30333117	A new bioinformatic approach to detect common 3D sites in protein structures.
Q60761703	A new catalog of protein β-sheets
Q27625016	A new fold in the scorpion toxin family, associated with an activity on a ryanodine-sensitive calcium channel
Q51627514	A new implicit solvent model for protein-ligand docking.
Q51980532	A new method for identification of protein (sub)families in a set of proteins based on hydropathy distribution in proteins
Q30426895	A new method for modeling large-scale rearrangements of protein domains
Q52235994	A new method for predicting binding free energy between receptor and ligand
Q98306758	A new method for protein characterization and classification using geometrical features for 3D face analysis: an example of tubulin structures
Q30328399	A new method to model membrane protein structure based on silent amino acid substitutions.
Q28647324	A new model for howO6-methylguanine-DNA methyltransferase binds DNA
Q51727987	A new pairwise folding potential based on improved decoy generation and side-chain packing
Q47304975	A new parameter-rich structure-aware mechanistic model for amino acid substitution during evolution.
Q47596335	A new perspective on analysis of helix-helix packing preferences in globular proteins
Q33412232	A new prediction strategy for long local protein structures using an original description
Q72303898	A new protein folding recognition potential function
Q27666111	A new regulatory switch in a JAK protein kinase
Q34417845	A new relaxed state in horse methemoglobin characterized by crystallographic studies
Q48055560	A new residue-nucleotide propensity potential with structural information considered for discriminating protein-RNA docking decoys
Q30415727	A new size-independent score for pairwise protein structure alignment and its application to structure classification and nucleic-acid binding prediction
Q37676135	A new structure-based classification of sulfide:quinone oxidoreductases.
Q47949421	A new subfamily of short bacterial adenylate kinases with the Mycobacterium tuberculosis enzyme as a model: A predictive and experimental study
Q57978665	A new subfamily of short bacterial adenylate kinases with theMycobacteriumtuberculosis enzyme as a model: A predictive and experimental study
Q30332170	A new test set for validating predictions of protein-ligand interaction.
Q34545038	A non-redundant protein-RNA docking benchmark version 2.0.
Q58482613	A novel TctA citrate transporter from an activated sludge metagenome: Structural and mechanistic predictions for the TTT family
Q33612052	A novel and efficient tool for locating and characterizing protein cavities and binding sites
Q42697595	A novel approach to local similarity of protein binding sites substantially improves computational drug design results
Q44784440	A novel approach to predict active sites of enzyme molecules
Q34296247	A novel approach to predicting protein structural classes in a (20-1)-D amino acid composition space
Q30382361	A novel approach to segregate and identify functional loop regions in protein structures using their Ramachandran maps.
Q47614703	A novel approach to the recognition of protein architecture from sequence using Fourier analysis and neural networks
Q90439071	A novel bacterial l-arginine sensor controlling c-di-GMP levels in Pseudomonas aeruginosa
Q35835565	A novel binding pocket of cyclin-dependent kinase 2.
Q30422991	A novel computer modeling approach to the structures of small bioactive peptides: the structure of gonadotropin releasing hormone
Q79252715	A novel cross-linked RNase A dimer with enhanced enzymatic properties
Q30326387	A novel energy-based stochastic method for positioning polar protons in protein structures from X-rays.
Q52078677	A novel exhaustive search algorithm for predicting the conformation of polypeptide segments in proteins
Q52036911	A novel fold recognition method using composite predicted secondary structures
Q51131839	A novel high resolution Calpha--Calpha distance dependent force field based on a high quality decoy set.
Q51644243	A novel measure characterized by a polar energy surface approximation for recognition and classification of transmembrane protein structures
Q30376830	A novel method for predicting and using distance constraints of high accuracy for refining protein structure prediction.
Q45966836	A novel method for protein secondary structure prediction using dual-layer SVM and profiles.
Q30408036	A novel method for protein–protein interaction site prediction using phylogenetic substitution models
Q68704266	A novel method for selective isolation of C-terminal peptides from tryptic digests of proteins by immobilized anhydrotrypsin: application to structural analyses of the tail sheath and tube proteins from bacteriophage T4
Q47867148	A novel method of resistance for influenza against a channel-blocking antiviral drug
Q43435701	A novel method to map and compare protein-protein interactions in spherical viral capsids.
Q27649771	A novel mode of dimerization via formation of a glutamate anhydride crosslink in a protein crystal structure
Q39113228	A novel parameterization scheme for energy equations and its use to calculate the structure of protein molecules
Q52018270	A novel shape complementarity scoring function for protein‐protein docking
Q30350110	A novel strategy for the identification of toxinlike structures in spider venom.
Q54766229	A novel twist on molecular interactions between thioredoxin and nicotinamide adenine dinucleotide phosphate-dependent thioredoxin reductase.
Q42607423	A novel “open‐form” structure of sortaseC from Streptococcus suis
Q30359373	A pair-to-pair amino acids substitution matrix and its applications for protein structure prediction.
Q51570605	A parameterized, continuum electrostatic model for predicting protein pKa values
Q71460525	A partial model of the erythropoietin receptor complex
Q30332485	A path from primary protein sequence to ligand recognition.
Q36836481	A peptide isolated by phage display binds to ICAM-1 and inhibits binding to LFA-1.
Q60167433	A perturbative view of protein structural variation
Q30336353	A pharmacophore docking algorithm and its application to the cross-docking of 18 HIV-NNRTI's in their binding pockets.
Q38515004	A pharmacophore-based evolutionary approach for screening selective estrogen receptor modulators
Q46814775	A phospho-sugar binding domain homologous to NagB enzymes regulates the activity of the central glycolytic genes repressor.
Q42676203	A phosphoinositide-binding sequence is shared by PH domain target molecules—a model for the binding of PH domains to proteins
Q47430872	A physical reference state unifies the structure-derived potential of mean force for protein folding and binding.
Q45028375	A portable allosteric mechanism
Q80678260	A potential molecular switch in an alpha-helical coiled coil
Q54563306	A potential processing enzyme in prokaryotes: Oligopeptidase B, a new type of serine peptidase
Q22061753	A practical overview of protein disorder prediction methods
Q46414948	A predicted consensus structure for the C terminus of the beta and gamma chains of fibrinogen
Q45168044	A predicted consensus structure for the N-terminal fragment of the heat shock protein HSP90 family
Q40978117	A predicted consensus structure for the protein kinase C2 homology (C2H) domain, the repeating unit of synaptotagmin
Q72416535	A prediction of the secondary structure of the pleckstrin homology domain
Q52256494	A predictive method for the evaluation of peptide binding in pocket 1 of HLA-DRB1 via global minimization of energy interactions
Q77894298	A preliminary CD and NMR study of the Escherichia coli DNA polymerase III theta subunit
Q42010167	A probabilistic model for secondary structure prediction from protein chemical shifts
Q57835079	A probabilistic network model for structural transitions in biomolecules
Q73326576	A probable conformational difference between recombinant and urinary erythropoietins
Q51800514	A proposed interaction mechanism between elastin-derived peptides and the elastin/laminin receptor-binding domain.
Q40774265	A proposed model for the PEX5-peroxisomal targeting signal-1 recognition complex
Q31710469	A protein dissection study demonstrates that two specific hydrophobic clusters play a key role in stabilizing the core structure of the molten globule state of human alpha-lactalbumin
Q27694677	A protein structural motif that bends DNA
Q34266948	A protein-RNA docking benchmark (I): nonredundant cases.
Q30415187	A protein-RNA docking benchmark (II): extended set from experimental and homology modeling data
Q52015253	A protein-protein docking benchmark
Q57897339	A protein-specifically adapted scoring function for the reranking of docking solutions
Q43033364	A quantum mechanics/molecular mechanics study of the reaction mechanism of the hepatitis C virus NS3 protease with the NS5A/5B substrate
Q30312627	A rapid method for exploring the protein structure universe
Q52206931	A rapid method for positioning small flexible molecules, nucleic acids, and large protein fragments in experimental electron density maps
Q56612167	A rapid method for positioning small flexible molecules, nucleic acids, and large protein fragments in experimental electron density maps
Q48103913	A rare polyglycine type II-like helix motif in naturally occurring proteins.
Q51799133	A recombinant allosteric lectin antagonist of HIV-1 envelope gp120 interactions
Q52007583	A reduced protein model with accurate native-structure identification ability
Q30421604	A reduced representation of proteins for use in restraint satisfaction calculations
Q40709394	A refined accuracy index to evaluate algorithms of protein secondary structure prediction
Q30010173	A residue in helical conformation in the native state adopts a β-strand conformation in the folding transition state despite its high and canonical Φ-value
Q57444427	A retrospective analysis of CASP2 threading predictions
Q74252593	A retrospective analysis of CASP2 threading predictions
Q42437093	A robust approach for analyzing a heterogeneous structural ensemble
Q30343009	A robust method to detect structural and functional remote homologues.
Q98897096	A rod conformation of the Pyrococcus furiosus Rad50 coiled coil
Q33763419	A role for indels in the evolution of Cro protein folds
Q27642418	A second binding site revealed by C-terminal truncation of calpain small subunit, a penta-EF-hand protein
Q31026460	A self-stabilized model of the chymotrypsin catalytic pocket. The energy profile of the overall catalytic cycle
Q47715192	A set of homology models of pore loop domain of six eukaryotic voltage-gated potassium channels Kv1.1-Kv1.6.
Q47625341	A set of van der Waals and coulombic radii of protein atoms for molecular and solvent-accessible surface calculation, packing evaluation, and docking
Q96339074	A shift of dynamic equilibrium between the KIT active and inactive states causes drug resistance
Q51897351	A simple and fuzzy method to align and compare druggable ligand-binding sites
Q44917503	A simple clustering algorithm can be accurate enough for use in calculations of pKs in macromolecules
Q41837828	A simple contact mapping algorithm for identifying potential peptide mimetics in protein-protein interaction partners
Q30353679	A simple measure of native-state topology and chain connectivity predicts the folding rates of two-state proteins with and without crosslinks.
Q33367761	A simple model of chaperonin-mediated protein folding
Q30427943	A simple probabilistic model of multibody interactions in proteins
Q43141142	A simple reference state makes a significant improvement in near-native selections from structurally refined docking decoys
Q58658653	A simple simulation model can reproduce the thermodynamic folding intermediate of apoflavodoxin
Q30342101	A simple topological representation of protein structure: implications for new, fast, and robust structural classification.
Q52276333	A simple two-dimensional representation for the common secondary structural elements of polypeptides and proteins
Q51917205	A simple way to compute protein dynamics without a mechanical model.
Q52380143	A simplified amino acid potential for use in structure predictions of proteins.
Q90388466	A single amino acid substitution alters ClpS2 binding specificity
Q43021401	A single proline substitution is critical for the thermostabilization of Clostridium beijerinckii alcohol dehydrogenase.
Q41809947	A single tryptic fragment of colicin E1 can form an ion channel: Stoichiometry confirms kinetics
Q52015262	A soft docking algorithm for predicting the structure of antibody-antigen complexes
Q52370464	A special-purpose computer for molecular dynamics: GRAPE-2A.
Q80518836	A statistical approach to the prediction of pK(a) values in proteins
Q31041065	A statistical framework to discover true associations from multiprotein complex pull-down proteomics data sets
Q47596105	A statistical rescoring scheme for protein-ligand docking: Consideration of entropic effect.
Q45771614	A strategy for theoretical binding constant, Ki, calculations for neuraminidase aromatic inhibitors designed on the basis of the active site structure of influenza virus neuraminidase.
Q93056692	A strong correlation between consensus sequences and unique super secondary structures in leucine rich repeats
Q33213914	A structural alphabet for local protein structures: improved prediction methods
Q38344133	A structural and dynamic model for the interaction of interleukin-8 and glycosaminoglycans: support from isothermal fluorescence titrations
Q57954836	A structural and functional dissection of the cardiac stress response factor MS1
Q44770740	A structural and thermodynamic escape mechanism from a drug resistant mutation of the HIV-1 protease
Q52425625	A structural assessment of the apo[a] protein of human lipoprotein[a]
Q30392692	A structural dissection of amino acid substitutions in helical transmembrane proteins
Q41097598	A structural model for human dihydrolipoamide dehydrogenase
Q30326075	A structural model for the rolA protein and its interaction with DNA.
Q30341941	A structural pattern-based method for protein fold recognition.
Q57209034	A study on protein sequence alignment quality
Q58796899	A substitution matrix for structural alphabet based on structural alignment of homologous proteins and its applications
Q62033064	A superposition free method for protein conformational ensemble analyses and local clustering based on a differential geometry representation of backbone
Q27730416	A surface mutant (G82R) of a human alpha-glutathione S-transferase shows decreased thermal stability and a new mode of molecular association in the crystal
Q84922862	A survey of hemoglobin quaternary structures
Q34249498	A synthetic hexapeptide designed to resemble a proteinaceous P-loop nest is shown to bind inorganic phosphate.
Q38739861	A systematic analysis of scoring functions in rigid-body protein docking: The delicate balance between the predictive rate improvement and the risk of overtraining
Q44273664	A systematic search for protein signature sequences
Q46330754	A tale of two tails: The importance of unstructured termini in the aggregation pathway of β2-microglobulin.
Q35784416	A temperature-dependent conformational change of NADH oxidase from Thermus thermophilus HB8.
Q44515176	A template search reveals mechanistic similarities and differences in beta-ketoacyl synthases (KAS) and related enzymes
Q34007562	A template-finding algorithm and a comprehensive benchmark for homology modeling of proteins
Q30319813	A tetrapeptide fragment-based design method results in highly stable artificial proteins
Q53780001	A tetrapeptide-based method for polyproline II-type secondary structure prediction
Q42646908	A theoretical DFT investigation of the lysozyme mechanism: computational evidence for a covalent intermediate pathway
Q71460506	A theoretical study of torsional flexibility in the active site of aspartic proteinases: implications for catalysis
Q30358633	A topologically related singularity suggests a maximum preferred size for protein domains.
Q30352330	A topology-constrained distance network algorithm for protein structure determination from NOESY data.
Q46354140	A tribute to Anna Tramontano (1957-2017).
Q53632809	A two-entropies analysis to identify functional positions in the transmembrane region of class A G protein-coupled receptors
Q30157444	A unified hydrophobicity scale for multispan membrane proteins
Q30953683	A unified representation of multiprotein complex data for modeling interaction networks
Q57972079	A unifold, mesofold, and superfold model of protein fold use
Q81319562	A unique and differential effect of denaturants on cofactor mediated activation of Plasmodium falciparum beta-ketoacyl-ACP reductase
Q27649477	A unique catalytic triad revealed by the crystal structure of APE0912, a short-chain dehydrogenase/reductase family protein from Aeropyrum pernix K1
Q34104980	A universal combinatorial design of antibody framework to graft distinct CDR sequences: A bioinformatics approach
Q47431327	A universal pathway for amyloid nucleus and precursor formation for insulin
Q52395596	A vector projection approach to predicting HIV protease cleavage sites in proteins
Q72303895	A vector projection method for predicting the specificity of GalNAc-transferase
Q69026449	A very short peptide makes a voltage-dependent ion channel: the critical length of the channel domain of colicin E1
Q29618211	A workbench for multiple alignment construction and analysis
Q48956120	A2T and A2V Aβ peptides exhibit different aggregation kinetics, primary nucleation, morphology, structure, and LTP inhibition
Q30351183	ABACUS, a direct method for protein NMR structure computation via assembly of fragments.
Q36745505	ACA-specific RNA sequence recognition is acquired via the loop 2 region of MazF mRNA interferase.
Q68837141	ALMA, an editor for large sequence alignments
Q46980211	ARTIST: an activated method in internal coordinate space for sampling protein energy landscapes
Q45127040	ATCUN-like metal-binding motifs in proteins: identification and characterization by crystal structure and sequence analysis
Q47985100	ATLAS: A database linking binding affinities with structures for wild-type and mutant TCR-pMHC complexes.
Q43286521	ATP conformations and ion binding modes in the active site of anthrax edema factor: a computational analysis.
Q41727106	ATP-activated oligomerization as a mechanism for apoptosis regulation: fold and mechanism prediction for CED-4.
Q36464322	ATP-binding to P-type ATPases as revealed by biochemical, spectroscopic, and crystallographic experiments
Q45139113	ATP-induced structural change of dephosphocoenzyme A kinase from Thermus thermophilus HB8.
Q51421505	ATTRACT: protein-protein docking in CAPRI using a reduced protein model
Q27652363	AU-rich RNA-binding induces changes in the quaternary structure of AUH
Q57838260	Ab initio calculations on hidden modulators of theta class glutathione transferase activity
Q39215060	Ab initio computational modeling of loops in G-protein-coupled receptors: lessons from the crystal structure of rhodopsin
Q44321996	Ab initio construction of polypeptide fragments: Accuracy of loop decoy discrimination by an all-atom statistical potential and the AMBER force field with the Generalized Born solvation model
Q52022174	Ab initio construction of polypeptide fragments: efficient generation of accurate, representative ensembles
Q50996693	Ab initio folding of extended α-helix: a theoretical study about the role of electrostatic polarization in the folding of helical structures
Q41696970	Ab initio folding of proteins using restraints derived from evolutionary information
Q71543075	Ab initio models for receptor-ligand interactions in proteins. 4. Model assembly study of the catalytic mechanism of triosephosphate isomerase
Q27673666	Ab initio phasing of a nucleoside hydrolase-related hypothetical protein from Saccharophagus degradans that is associated with carbohydrate metabolism
Q46862322	Ab initio prediction of peptide-MHC binding geometry for diverse class I MHC allotypes
Q30330293	Ab initio prediction of protein structure using LINUS.
Q33210184	Ab initio prediction of the three-dimensional structure of a de novo designed protein: a double-blind case study
Q86983476	Ab initio protein folding simulations using atomic burials as informational intermediates between sequence and structure
Q52280917	Ab initio protein folding simulations with genetic algorithms: Simulations on the complete sequence of small proteins
Q28261756	Ab initio protein structure assembly using continuous structure fragments and optimized knowledge‐based force field
Q28145980	Ab initio protein structure prediction of CASP III targets using ROSETTA
Q30323186	Ab initio protein structure prediction using a combined hierarchical approach.
Q30328051	Ab initio protein structure prediction using physicochemical potentials and a simplified off-lattice model.
Q30329572	Ab initio protein structure prediction via a combination of threading, lattice folding, clustering, and structure refinement.
Q52324541	Ab initio structure prediction for small polypeptides and protein fragments using genetic algorithms
Q85744307	Ab initio structure prediction of the antibody hypervariable H3 loop
Q41451876	AbDesign: An algorithm for combinatorial backbone design guided by natural conformations and sequences.
Q33559036	Aberrant coordination geometries discovered in the most abundant metalloproteins
Q45028389	Absence of kinetic thermal stabilization in a hyperthermophile rubredoxin indicated by 40 microsecond folding in the presence of irreversible denaturation
Q46798591	Absolute and relative binding free energy calculations of the interaction of biotin and its analogs with streptavidin using molecular dynamics/free energy perturbation approaches
Q30386091	Absolute binding free energy calculations: on the accuracy of computational scoring of protein-ligand interactions
Q30400320	Absolute quality evaluation of protein model structures using statistical potentials with respect to the native and reference states.
Q84511287	Abundance and functional roles of intrinsic disorder in allergenic proteins and allergen representative peptides
Q48194197	Accelerated molecular dynamics simulations of the octopamine receptor using GPUs: discovery of an alternate agonist-binding position.
Q78136382	Accessibility and order of water sites in and around proteins: A crystallographic time-averaging study
Q44632578	Accessibility of oxygen with respect to the heme pocket in horseradish peroxidase.
Q57642963	Accessibility of tobacco lipid transfer protein cavity revealed by 15N NMR relaxation studies and molecular dynamics simulations
Q53954493	Accessibility to internal cavities and ligand binding sites monitored by protein crystallographic thermal factors
Q71313776	Accessing the Kabat antibody sequence database by computer
Q90623611	Accessory mutations balance the marginal stability of the HIV-1 protease in drug resistance
Q43973743	Accommodation of single amino acid insertions by the native state of staphylococcal nuclease
Q51629030	Accounting for conformational entropy in predicting binding free energies of protein-protein interactions
Q33274715	Accounting for ligand-bound metal ions in docking small molecules on adenylyl cyclase toxins
Q51300167	Accounting for loop flexibility during protein-protein docking
Q30428156	Accuracy and precision of NMR relaxation experiments and MD simulations for characterizing protein dynamics
Q40950814	Accuracy and reliability of the scaling-relaxation method for loop closure: an evaluation based on extensive and multiple copy conformational samplings
Q36554207	Accuracy issues involved in modeling in vivo protein structures using PM7.
Q59536347	Accuracy of binding mode prediction with a cascadic stochastic tunneling method
Q58533574	Accuracy of protein flexibility predictions
Q30353159	Accuracy of sequence alignment and fold assessment using reduced amino acid alphabets.
Q30431722	Accuracy of side-chain prediction upon near-native protein backbones generated by Ab initio folding methods
Q47715101	Accurate and efficient description of protein vibrational dynamics: comparing molecular dynamics and Gaussian models
Q30377100	Accurate contact predictions using covariation techniques and machine learning.
Q45805551	Accurate domain identification with structure-anchored hidden Markov models, saHMMs
Q71763589	Accurate general method for lattice approximation of three-dimensional structure of a chain molecule
Q47191490	Accurate geometries for "mountain pass" regions of the Ramachandran plot using quantum chemical calculations.
Q30373257	Accurate prediction for atomic-level protein design and its application in diversifying the near-optimal sequence space.
Q45959496	Accurate prediction of hot spot residues through physicochemical characteristics of amino acid sequences.
Q51127920	Accurate prediction of interfacial residues in two-domain proteins using evolutionary information: implications for three-dimensional modeling
Q51699017	Accurate prediction of protein folding rates from sequence and sequence-derived residue flexibility and solvent accessibility
Q30342423	Accurate prediction of solvent accessibility using neural networks-based regression.
Q41755871	Accurate reconstruction of all-atom protein representations from side-chain-based low-resolution models
Q30366585	Accurate single-sequence prediction of solvent accessible surface area using local and global features
Q48022610	Accurate template-based modeling in CASP12 using the IntFOLD4-TS, ModFOLD6, and ReFOLD methods
Q73083577	Acetyl-CoA enolization in citrate synthase: a quantum mechanical/molecular mechanical (QM/MM) study
Q34592447	Achieving 80% ten-fold cross-validated accuracy for secondary structure prediction by large-scale training.
Q34522304	Achieving reliability and high accuracy in automated protein docking: ClusPro, PIPER, SDU, and stability analysis in CAPRI rounds 13-19
Q52243379	Acid helix-turn activator motif
Q69444361	Acid-induced dimerization of skeletal troponin C
Q53575719	Acid-induced loss of functional properties of bacterial cell division protein FtsZ: evidence for an alternative conformation at acidic pH.
Q30364207	Acidic groups docked to well defined wetted pockets at the core of the binding interface: a tale of scoring and missing protein interactions in CAPRI.
Q51896285	Acidic range titration of HEWL using a constant-pH molecular dynamics method
Q40163889	Activation loop phosphorylation-independent kinase activity of human protein kinase C zeta
Q41652285	Activation of blood coagulation factor VIIa with cleaved tissue factor extracellular domain and crystallization of the active complex
Q69826675	Activation of retinal rod cyclic GMP-phosphodiesterase by transducin: characterization of the complex formed by phosphodiesterase inhibitor and transducin alpha-subunit
Q27657593	Active and inactive state structures of unliganded Lactobacillus casei allosteric L-lactate dehydrogenase
Q44026702	Active site conformation in myoglobin as determined by X-ray absorption spectroscopy
Q42613455	Active site dynamics of acyl-chymotrypsin
Q54069115	Activity of crystalline turkey egg white lysozyme
Q30328049	Adaptations of the helix-grip fold for ligand binding and catalysis in the START domain superfamily.
Q50951079	Adaptive Smith-Waterman residue match seeding for protein structural alignment
Q74177440	Addendum to crystal structure of recombinant trypsin-solubilized fragment of cytochrome b(5) and the structural comparison with Val61His mutant
Q39062782	Addressing recent docking challenges: A hybrid strategy to integrate template-based and free protein-protein docking.
Q30350426	Addressing the intrinsic disorder bottleneck in structural proteomics.
Q30323173	Addressing the issue of sequence-to-structure alignments in comparative modeling of CASP3 target proteins.
Q30328398	Adenine recognition: a motif present in ATP-, CoA-, NAD-, NADP-, and FAD-dependent proteins.
Q73594394	Adipyl crosslinked bovine hemoglobins as new models of allosteric systems
Q44960719	Adjacent cysteines are capable of ligating the same tetranuclear iron-sulfur cluster
Q46212567	Adjusting potential energy functions for lattice models of chain molecules
Q28141081	Adrenodoxin: structure, stability, and electron transfer properties
Q46917279	Adsorption and folding dynamics of MPER of HIV-1 gp41 in the presence of DPC micelle.
Q30402449	Advances in molecular engineering of carbohydrate-binding modules.
Q54617905	Affinities of phosphorylated substrates for the E. coli tryptophan synthase alpha-subunit: roles of Ser-235 and helix-8' dipole.
Q70388089	Affinity of nonhomologous amphiphilic peptides toward a monoclonal antibody raised against apolipoprotein A-I
Q40664616	Age-related cleavages of crystallins in human lens cortical fiber cells generate a plethora of endogenous peptides and high molecular weight complexes.
Q91245002	AggScore: Prediction of aggregation-prone regions in proteins based on the distribution of surface patches
Q54356548	Aggregating the amyloid Abeta(11-25) peptide into a four-stranded beta-sheet structure
Q59673231	Aggregation of small peptides studied by molecular dynamics simulations
Q31170430	Aggregation prone regions in human proteome: Insights from large-scale data analyses
Q34543978	Alanine and proline content modulate global sensitivity to discrete perturbations in disordered proteins
Q73062328	Aldose and aldehyde reductases: correlation of molecular modeling and mass spectrometric studies on the binding of inhibitors to the active site
Q44403946	Algorithms for computational solvent mapping of proteins
Q50563601	Aligning, analyzing, and visualizing sequences for antibody engineering: Automated recognition of immunoglobulin variable region features
Q77538024	Alignments grow, secondary structure prediction improves
Q48440493	Alkaline phosphatase-somatostatin hybrid proteins as probes for somatostatin-14 receptors
Q39276813	All-atom and coarse-grained simulations of the forced unfolding pathways of the SNARE complex.
Q83003785	All-atom chain-building by optimizing MODELLER energy function using conformational space annealing
Q78434116	All-atom fast protein folding simulations: the villin headpiece
Q30343744	All-atom folding of the three-helix HIV accessory protein with an adaptive parallel tempering method.
Q90564442	All-atom molecular dynamics simulations reveal how kinesin transits from one-head-bound to two-heads-bound state
Q46718310	All-atom replica exchange molecular simulation of protein BBL.
Q91895799	All-atom structure ensembles of islet amyloid polypeptides determined by enhanced sampling and experiment data restraints
Q44165223	Allosteric effects of chloride ions at the intradimeric alpha1beta1 and alpha2beta2 interfaces of human hemoglobin
Q34032620	Allosteric effects of the antipsychotic drug trifluoperazine on the energetics of calcium binding by calmodulin
Q43629661	Allosteric free energy changes at the alpha 1 beta 2 interface of human hemoglobin probed by proton exchange of Trp beta 37.
Q45346177	Allosteric regulation of PKCθ: understanding multistep phosphorylation and priming by ligands in AGC kinases
Q46786473	Allosteric sites can be identified based on the residue-residue interaction energy difference
Q50887279	Allosteric transitions of ATP-binding cassette transporter MsbA studied by the adaptive anisotropic network model.
Q30380931	Allostery and conformational free energy changes in human tryptophanyl-tRNA synthetase from essential dynamics and structure networks.
Q53123409	All‐atom structural models of insulin binding to the insulin receptor in the presence of a tandem hormone‐binding element
Q72335558	Alpha helix capping in synthetic model peptides by reciprocal side chain-main chain interactions: evidence for an N terminal "capping box"
Q47921655	Alpha helix shortening in 1522 MSP-1 conserved peptide analogs is associated with immunogenicity and protection against P. falciparum malaria
Q30351250	Alpha-alpha linking motifs and interhelical orientations.
Q31813824	Alpha-amylase inhibitors selected from a combinatorial library of a cellulose binding domain scaffold
Q37918087	Alpha-helical coiled coils and bundles: how to design an alpha-helical protein
Q83932055	Alpha-helix stabilization by alanine relative to glycine: roles of polar and apolar solvent exposures and of backbone entropy
Q72200807	Alpha-helix-forming propensities in peptides and proteins
Q47992535	Alpha/beta-hydrolases: A unique structural motif coordinates catalytic acid residue in 40 protein fold families
Q107864575	AlphaFold2 predicts the inward‐facing conformation of the multidrug transporter LmrP
Q81603069	Alteration of protein subcellular location and domain formation by alternative translational initiation
Q48312992	Altered dynamics upon oligomerization corresponds to key functional sites.
Q35803157	Altered nuclear cofactor switching in retinoic‐resistant variants of the PML‐RARα oncoprotein of acute promyelocytic leukemia
Q33302442	Altering the laccase functionality by in vivo assembly of mutant libraries with different mutational spectra
Q46456745	Alternate succession of steps can lead to the folding of a multidomain oligomeric protein
Q30342103	Alternative alignments from comparison of protein structures.
Q46102425	Alternative zinc-binding sites explain the redox sensitivity of zinc-containing anti-sigma factors
Q47810376	AmbiPack: A systematic algorithm for packing of macromolecular structures with ambiguous distance constraints
Q30379551	Amino acid alphabet reduction preserves fold information contained in contact interactions in proteins.
Q43017132	Amino acid coupling patterns in thermophilic proteins
Q46049108	Amino acid function relates to its embedded protein microenvironment: A study on disulfide-bridged cystine
Q57739954	Amino acid pairing at the N- and C-termini of helical segments in proteins
Q30380675	Amino acid positions subject to multiple coevolutionary constraints can be robustly identified by their eigenvector network centrality scores
Q54463670	Amino acid residues that determine functional specificity of NADP- and NAD-dependent isocitrate and isopropylmalate dehydrogenases.
Q51919300	Amino acid sequence autocorrelation vectors and Bayesian-regularized genetic neural networks for modeling protein conformational stability: gene V protein mutants
Q47349668	Amino acid sequence predicts folding rate for middle-size two-state proteins
Q46084397	Amino acid substitution analysis of E. coli thymidylate synthase: the study of a highly conserved region at the N-terminus
Q30354410	Amino acid substitutions affecting protein dynamics in eglin C do not affect heat capacity change upon unfolding.
Q82692307	Amino acid substitutions at protein-protein interfaces that modulate the oligomeric state
Q69729591	Amino acid substitutions that increase the thermal stability of the lambda Cro protein
Q37987535	Amphipathic helix motif: classes and properties
Q29543244	Amphipathic α-helices in proteins: Results from analysis of protein structures
Q50497689	Amyloid aggregation of lysozyme: The synergy study of red wine polyphenols
Q51910115	An NMA-guided path planning approach for computing large-amplitude conformational changes in proteins
Q91793239	An NMR and MD study of complexes of bacteriophage lambda lysozyme with tetra- and hexa-N-acetylchitohexaose
Q54359608	An NMR study of the N-terminal domain of wild-type hERG and a T65P trafficking deficient hERG mutant
Q30984170	An NMR-based molecular dynamics simulation of the interaction of the lac repressor headpiece and its operator in aqueous solution
Q51638608	An accurate feature-based method for identifying DNA-binding residues on protein surfaces.
Q83452854	An accurate model of polyglutamine
Q45559122	An algorithm for determining the conformation of polypeptide segments in proteins by systematic search
Q42554397	An all-atom knowledge-based energy function for protein-DNA threading, docking decoy discrimination, and prediction of transcription-factor binding profiles
Q30157501	An all-atom structure-based potential for proteins: bridging minimal models with all-atom empirical forcefields
Q28271509	An all-atom, distance-dependent scoring function for the prediction of protein-DNA interactions from structure
Q27648910	An alternate sucrose binding mode in the E203Q Arabidopsis invertase mutant: an X-ray crystallography and docking study
Q30846455	An alternative view of protein fold space
Q41970502	An amino acid code for irregular and mixed protein packing
Q41835427	An amino acid code for β-sheet packing structure.
Q30381456	An amino acid code to define a protein's tertiary packing surface.
Q28305576	An amino acid has two sides: a new 2D measure provides a different view of solvent exposure
Q48468420	An analysis approach to identify specific functional sites in orthologous proteins using sequence and structural information: application to neuroserpin reveals regions that differentially regulate inhibitory activity
Q52340732	An analysis of side chain interactions and pair correlations within antiparallel beta-sheets: the differences between backbone hydrogen-bonded and non-hydrogen-bonded residue pairs
Q42614512	An analysis of the conformational paths of citrate synthase
Q52074685	An analysis of the helix-to-strand transition between peptides with identical sequence.
Q34106069	An ancient anion-binding structural module in RNA and DNA helicases
Q30351280	An assessment of the accuracy of methods for predicting hydrogen positions in protein structures.
Q27648766	An asymmetric dimer of beta-lactoglobulin in a low humidity crystal form--structural changes that accompany partial dehydration and protein action
Q80594685	An atomic resolution structure for human fibroblast growth factor 1
Q73864393	An atoms-in-molecules study of the genetically-encoded amino acids: I. Effects of conformation and of tautomerization on geometric, atomic, and bond properties
Q30323188	An attempt to analyse progress in fold recognition from CASP1 to CASP3.
Q27644751	An autoantibody to single-stranded DNA: Comparison of the three-dimensional structures of the unliganded fab and a deoxynucleotide-fab complex
Q80443351	An automated decision-tree approach to predicting protein interaction hot spots
Q42692720	An automated method for consistent helix assignment using turn information.
Q52322027	An automated method for dynamic ligand design
Q38232597	An effective coarse-grained model for biological simulations: recent refinements and validations
Q33256083	An efficient and generic strategy for producing soluble human proteins and domains in E. coli by screening construct libraries
Q30365631	An efficient conformational sampling method for homology modeling.
Q43016309	An electrostatic basis for the stability of thermophilic proteins
Q34365419	An empirical energy function for threading protein sequence through the folding motif
Q78010864	An empirical energy potential with a reference state for protein fold and sequence recognition
Q52018277	An empirical model for electrostatic interactions in proteins incorporating multiple geometry‐dependent dielectric constants
Q34265765	An energy-based conformer library for side chain optimization: improved prediction and adjustable sampling
Q46489564	An engineered folded PLP-bound monomer of Treponema denticola cystalysin reveals the effect of the dimeric structure on the catalytic properties of the enzyme
Q82424690	An enhanced elastic network model to represent the motions of domain-swapped proteins
Q57137624	An evaluation of implicit and explicit solvent model systems for the molecular dynamics simulation of bacteriophage T4 lysozyme
Q57752477	An evolutionary and structure-based docking model for glucocerebrosidase-saposin C and glucocerebrosidase-substrate interactions - relevance for Gaucher disease
Q34425600	An evolutionary treasure: unification of a broad set of amidohydrolases related to urease
Q52507508	An expectation maximization (EM) algorithm for the identification and characterization of common sites in unaligned biopolymer sequences
Q54577829	An extended sampling of the configurational space of HPr from E. coli.
Q30421279	An improved pair potential to recognize native protein folds
Q30333352	An improved protein decoy set for testing energy functions for protein structure prediction.
Q51897089	An insight into the general relationship between the three dimensional structures of enzymes and their electronic wave functions: Implication for the prediction of functional sites of enzymes
Q58112061	An insight of early PrP-E200K aggregation by combined molecular dynamics/fragment molecular orbital approaches
Q27653168	An intact SAM-dependent methyltransferase fold is encoded by the human endothelin-converting enzyme-2 gene
Q27689465	An integrated approach for thermal stabilization of a mesophilic adenylate kinase
Q33669063	An integrated approach to inferring gene-disease associations in humans
Q34188571	An integrated suite of fast docking algorithms
Q27678283	An intersubunit disulfide bridge stabilizes the tetrameric nucleoside diphosphate kinase of Aquifex aeolicus
Q51961972	An intuitive approach to measuring protein surface curvature.
Q80626080	An iterative knowledge-based scoring function for protein-protein recognition
Q60668711	An iterative structure-assisted approach to sequence alignment and comparative modeling
Q52141283	An iterative structure-assisted approach to sequence alignment and comparative modeling.
Q39698701	An optimized MM/PBSA virtual screening approach applied to an HIV-1 gp41 fusion peptide inhibitor.
Q92315987	An overview of data-driven HADDOCK strategies in CAPRI rounds 38-45
Q116729526	An overview of the Plasmodium falciparum hexose transporter and its therapeutic interventions
Q40161441	An unsuspected ecdysteroid/steroid phosphatase activity in the key T-cell regulator, Sts-1: surprising relationship to insect ecdysteroid phosphate phosphatase
Q44898256	An unusual triosephosphate isomerase from the early divergent eukaryote Giardia lamblia.
Q41940863	An unusually small dimer interface is observed in all available crystal structures of cytosolic sulfotransferases
Q27702504	Anabaena sp. DyP-type peroxidase is a tetramer consisting of two asymmetric dimers
Q58621984	Anabaenaapoflavodoxin hydrogen exchange: On the stable exchange core of the α/β(21345) flavodoxin-like family
Q51068333	Analycys: a database for conservation and conformation of disulphide bonds in homologous protein domains
Q89915418	Analyses of protein cores reveal fundamental differences between solution and crystal structures
Q54627051	Analyses of the folding properties of ferredoxin-like fold proteins by means of a coarse-grained Gō model: relationship between the free energy profiles and folding cores.
Q30794988	Analysis and assessment of ab initio three-dimensional prediction, secondary structure, and contacts prediction
Q47616798	Analysis and assessment of comparative modeling predictions in CASP4.
Q45623134	Analysis and network representation of hotspots in protein interfaces using minimum cut trees.
Q52933950	Analysis and prediction of helix-helix interactions in membrane channels and transporters
Q30367312	Analysis and prediction of protein local structure based on structure alphabets.
Q30421316	Analysis of C alpha geometry in protein structures
Q44817530	Analysis of CDK2 active-site hydration: a method to design new inhibitors
Q84524231	Analysis of Ca2+/Mg2+ selectivity in alpha-lactalbumin and Ca(2+)-binding lysozyme reveals a distinct Mg(2+)-specific site in lysozyme
Q45279346	Analysis of GTPases carrying hydrophobic amino acid substitutions in lieu of the catalytic glutamine: implications for GTP hydrolysis
Q77435969	Analysis of N-terminal capping using carbonyl-carbon chemical shift measurements
Q30363498	Analysis of TASSER-based CASP7 protein structure prediction results.
Q30328086	Analysis of a data set of paired uncomplexed protein structures: new metrics for side-chain flexibility and model evaluation.
Q114234888	Analysis of amyloidogenic transthyretin mutations using continuum solvent free energy calculations
Q56901077	Analysis of antibodies of known structure suggests a lack of correspondence between the residues in contact with the antigen and those modified by somatic hypermutation
Q51922352	Analysis of chameleon sequences and their implications in biological processes
Q74252586	Analysis of comparative modeling predictions for CASP2 targets 1, 3, 9, and 17
Q46754270	Analysis of correlated domain motions in IgG light chain reveals possible mechanisms of immunological signal transduction
Q47898390	Analysis of deep learning methods for blind protein contact prediction in CASP12.
Q93026322	Analysis of distance-based protein structure prediction by deep learning in CASP13
Q48709850	Analysis of domain motions by approximate normal mode calculations
Q58008923	Analysis of domain motions in large proteins
Q34794325	Analysis of electrostatic contributions to the selectivity of interactions between RING-finger domains and ubiquitin-conjugating enzymes
Q54353016	Analysis of electrostatic interactions in the denatured state ensemble of the N-terminal domain of L9 under native conditions
Q30380565	Analysis of free modeling predictions by RBO aleph in CASP11.
Q27652879	Analysis of nasturtium TmNXG1 complexes by crystallography and molecular dynamics provides detailed insight into substrate recognition by family GH16 xyloglucan endo-transglycosylases and endo-hydrolases
Q57133878	Analysis of pH-dependent elements in proteins: geometry and properties of pairs of hydrogen-bonded carboxylic acid side-chains
Q38501868	Analysis of protein function and its prediction from amino acid sequence
Q36014909	Analysis of protein homology by assessing the (dis)similarity in protein loop regions
Q52423082	Analysis of protein sheet topologies by graph theoretical methods
Q52007585	Analysis of protein structures reveals regions of rare backbone conformation at functional sites.
Q51602292	Analysis of proton wires in the enzyme active site suggests a mechanism of c-di-GMP hydrolysis by the EAL domain phosphodiesterases.
Q42537687	Analysis of secondary structure and self-assembly of amelogenin by variable temperature circular dichroism and isothermal titration calorimetry
Q52141082	Analysis of sequence signature defining functional specificity and structural stability in helix-loop-helix proteins
Q45205601	Analysis of sequence-reactivity space for protein-protein interactions
Q81413470	Analysis of similarity/dissimilarity of protein sequences
Q42609804	Analysis of singleton ORFans in fully sequenced microbial genomes
Q42635906	Analysis of six protein structures predicted by comparative modeling techniques
Q44929415	Analysis of solvent structure in proteins using neutron D2O-H2O solvent maps: pattern of primary and secondary hydration of trypsin
Q44242211	Analysis of the binding energies of testosterone, 5alpha-dihydrotestosterone, androstenedione and dehydroepiandrosterone sulfate with an antitestosterone antibody
Q44464205	Analysis of the differences in the folding kinetics of structurally homologous proteins based on predictions of the gross features of residue contacts
Q43069600	Analysis of the electrochemistry of hemes with E(m)s spanning 800 mV.
Q34254489	Analysis of the linker region joining the adenylation and carrier protein domains of the modular nonribosomal peptide synthetases.
Q84583065	Analysis of the movements of helices in EF-hands
Q34727787	Analysis of the peroxiredoxin family: using active-site structure and sequence information for global classification and residue analysis
Q30429654	Analysis of the predicted structures of domain 1 of protein g3 (T0030) and NK‐lysin (T0042)
Q48207992	Analysis of the products of genes encompassed by the theoretically predicted pathogenicity islands of Mycobacterium tuberculosis and Mycobacterium bovis.
Q53516474	Analysis of the protein kinome of Entamoeba histolytica
Q30367758	Analysis of the residue-residue coevolution network and the functionally important residues in proteins.
Q43728443	Analysis of the segmental stability of helical peptides by isotope-edited infrared spectroscopy
Q44209003	Analysis of the sequence and structural features of the left-handed beta-helical fold
Q60913981	Analysis of the steric strain in the polypeptide backbone of protein molecules
Q52276346	Analysis of the structure of HIV-1 protease complexed with a hexapeptide inhibitor. Part II: Molecular dynamic studies of the active site region
Q36849662	Analysis of the structure of chemically synthesized HIV-1 protease complexed with a hexapeptide inhibitor. Part I: Crystallographic refinement of 2 A data.
Q27650208	Analysis of the structure of human apo-S100B at low temperature indicates a unimodal conformational distribution is adopted by calcium-free S100 proteins
Q52302212	Analysis of topological and nontopological structural similarities in the PDB: new examples with old structures
Q54591150	Analysis of water patterns in protein kinase binding sites.
Q57991167	Analysis of zinc-ligand bond lengths in metalloproteins: Trends and patterns
Q46114043	Analysis on folding of misgurin using two-dimensional HP model
Q42201409	Analysis on long-range residue-residue communication using molecular dynamics
Q51647257	Analytical shape computation of macromolecules: I. molecular area and volume through alpha shape
Q51647253	Analytical shape computation of macromolecules: II. Inaccessible cavities in proteins
Q46823177	Analyzing and modeling the inhibitory effect of phosphatidic acid on the GTP-gamma-S binding activity of Goalpha
Q83159754	Analyzing large-scale structural change in proteins: comparison of principal component projection and Sammon mapping
Q52214947	Analyzing protein circular dichroism spectra for accurate secondary structures
Q113555581	Analyzing protein circular dichroism spectra for accurate secondary structures
Q46920266	Analyzing the catalytic mechanism of MPtpA: a low molecular weight protein tyrosine phosphatase from Mycobacterium tuberculosis through site-directed mutagenesis
Q51050680	Analyzing the effect of homogeneous frustration in protein folding.
Q56770481	Anatomy of a structural pathway for activation of the catalytic domain of Src kinase Hck
Q44566271	Anatomy of specific interactions between lambda repressor and operator DNA.
Q27643235	Ancestral sequence evolutionary trace and crystal structure analyses of alkaline alpha-amylase from Bacillus sp. KSM-1378 to clarify the alkaline adaptation process of proteins
Q80962906	Anchor profiles of HLA-specific peptides: analysis by a novel affinity scoring method and experimental validation
Q46600393	Anchoring effects in a wide binding pocket: the molecular basis of regioselectivity in engineered cytochrome P450 monooxygenase from B. megaterium.
Q47804956	Anion induced conformational preference of Cα NN motif residues in functional proteins
Q73798402	Anion-induced stabilization of human serum albumin prevents the formation of intermediate during urea denaturation
Q53665755	Anisotropic effective interactions in a coarse-grained tube picture of proteins
Q68697933	Anisotropy and anharmonicity of atomic fluctuations in proteins: analysis of a molecular dynamics simulation
Q33289747	Annexin A2/P11 interaction: new insights into annexin A2 tetramer structure by chemical crosslinking, high-resolution mass spectrometry, and computational modeling
Q46701909	Anomalies in the ionic properties of serum albumin
Q83003932	Another look at the conditions for the extraction of protein knowledge-based potentials
Q45777876	Antagonist binding and induced conformational dynamics of GPCR A2A adenosine receptor
Q46036599	Anti-apoptotic Bcl-XL protein in complex with BH3 peptides of pro-apoptotic Bak, Bad, and Bim proteins: comparative molecular dynamics simulations.
Q33425252	Anti-cooperativity and cooperativity in hydrophobic interactions: Three-body free energy landscapes and comparison with implicit-solvent potential functions for proteins
Q30835904	Anti-idiotypic protein domains selected from protein A-based affibody libraries
Q86705196	Antiapoptotic Bcl-2 homolog CED-9 in Caenorhabditis elegans: dynamics of BH3 and CED-4 binding regions and comparison with mammalian antiapoptotic Bcl-2 proteins
Q41172450	Antibodies as a model system for comparative model refinement.
Q52206838	Antibody BCF2 against scorpion toxin Cn2 from Centuroides noxius Hoffmann: primary structure and three-dimensional model as free Fv fragment and complexed with its antigen
Q58665182	Antibody BCF2 against scorpion toxin cn2 fromCentruroides noxius hoffmann: Primary structure and three-dimensional model as free fv fragment and complexed with its antigen
Q27674338	Antibody modeling assessment
Q27689511	Antibody modeling assessment II. Structures and models
Q44898263	Antibody recognition of chiral surfaces. Structural models of antibody complexes with leucine-leucine-tyrosine crystal surfaces
Q47214903	Antibody side chain conformations are position-dependent
Q30360105	Antibody structure determination using a combination of homology modeling, energy-based refinement, and loop prediction.
Q89749874	Anticodon-binding domain swapping in a nondiscriminating aspartyl-tRNA synthetase reveals contributions to tRNA specificity and catalytic activity
Q92039566	Antimicrobial activity and structure of a consensus human β-defensin and its comparison to a novel putative hBD10
Q46764629	Apo-parvalbumin as an intrinsically disordered protein
Q68763755	Apolar peptide models for conformational heterogeneity, hydration, and packing of polypeptide helices: crystal structure of hepta- and octapeptides containing alpha-aminoisobutyric acid
Q44898266	Apolipoprotein E-low density lipoprotein receptor binding: study of protein-protein interaction in rationally selected docked complexes
Q40553676	Application of 3D-Jury, GRDB, and Verify3D in fold recognition
Q28133308	Application of InChI to curate, index, and query 3-D structures
Q30329571	Application of PROSPECT in CASP4: characterizing protein structures with new folds.
Q43804448	Application of a directed conformational search for generating 3-D coordinates for protein structures from alpha-carbon coordinates
Q51679184	Application of biasing-potential replica-exchange simulations for loop modeling and refinement of proteins in explicit solvent
Q90321405	Application of docking methodologies to modeled proteins
Q45752370	Application of electrospray ionization mass spectrometry for studying human immunodeficiency virus protein complexes
Q30367324	Application of information theory to a three-body coarse-grained representation of proteins in the PDB: insights into the structural and evolutionary roles of residues in protein structure.
Q51607223	Application of long‐range order to predict unfolding rates of two‐state proteins
Q29614377	Application of multiple sequence alignment profiles to improve protein secondary structure prediction
Q37480652	Application of nonlinear dimensionality reduction to characterize the conformational landscape of small peptides
Q57128603	Application of the Gaussian dielectric boundary in Zap to the prediction of protein pKa values
Q47762472	Application of the fuzzy-oil-drop model to membrane protein simulation
Q42041433	Applying Undertaker to quality assessment
Q43490153	Applying conformational selection theory to improve crossdocking efficiency in 3-phosphoinositide dependent protein kinase-1.
Q30373263	Applying undertaker cost functions to model quality assessment.
Q47606431	Approaching the CAPRI challenge with an efficient geometry-based docking
Q48256361	Aquerium: A web application for comparative exploration of domain-based protein occurrences on the taxonomically clustered genome tree
Q47773583	Archaea S-layer nanotube from a "black smoker" in complex with cyclo-octasulfur (S8 ) rings
Q99553561	Archaeal roots of intramembrane aspartyl protease siblings signal peptide peptidase and presenilin
Q46650298	Archeal lectins: An identification through a genomic search
Q103739890	Are Granulins Copper Sequestering Proteins?
Q30363491	Are aromatic carbon donor hydrogen bonds linear in proteins?
Q30430535	Are knowledge-based potentials derived from protein structure sets discriminative with respect to amino acid types?
Q58024676	Are knowledge-based potentials derived from protein structure sets discriminative with respect to amino acid types?
Q52913168	Are membrane proteins "inside-out" proteins?
Q51960314	Are structural biases at protein termini a signature of vectorial folding?
Q57000452	Are there dominant membrane protein families with a given number of helices?
Q88162775	Arginine side chain stacking with peptide plane stabilizes the protein helix conformation in a cooperative way
Q77771890	Arm-domain interactions in proteins: a review
Q43728440	Aromatic di-alanine repeats (AdAR) are structural motifs characteristic of the soluble N-ethylmaleimide-sensitive factor attachment protein (SNAP) family
Q43503098	Aromatic interactions in homeodomains contribute to the low quantum yield of a conserved, buried tryptophan
Q44125151	Aromatic side-chain interactions in proteins. I. Main structural features
Q44125153	Aromatic side-chain interactions in proteins. II. Near- and far-sequence Phe-X pairs
Q44745629	Aromatic side-chain interactions in proteins: near- and far-sequence Tyr-X pairs
Q98161413	Artificial protein sequences enable recognition of vicinal and distant protein functional relationships
Q30008902	Artificial proteins as allosteric modulators of PDZ3 and SH3 in two-domain constructs: A computational characterization of novel chimeric proteins
Q57469526	Asp271 is critical for substrate interaction with the surface binding site in β-agarase A from Zobellia galactanivorans
Q30411473	Asparagine and glutamine differ in their propensities to form specific side chain‐backbone hydrogen bonded motifs in proteins
Q79935408	Assay for rapid analysis of the tri-peptidase activity of LTA4 hydrolase
Q57851675	Assembling novel protein folds from super-secondary structural fragments
Q47826690	Assembly factors of F1FO-ATP synthase across genomes.
Q44875749	Assembly of a tetrameric alpha-helical bundle: computer simulations on an intermediate-resolution protein model
Q30431371	Assembly of protein structure from sparse experimental data: An efficient Monte Carlo model
Q73589794	Assembly of protein tertiary structures from secondary structures using optimized potentials
Q81383344	Assembly of the oncogenic DNA-binding complex LMO2-Ldb1-TAL1-E12
Q33248321	Assembly of transmembrane helices of simple polytopic membrane proteins from sequence conservation patterns
Q30352380	Assessing a novel approach for predicting local 3D protein structures from sequence.
Q44060639	Assessing equilibration and convergence in biomolecular simulations
Q80638893	Assessing model accuracy using the homology modeling automatically software
Q81635428	Assessing precision and accuracy of protein structures derived from NMR data
Q36312787	Assessing protein disorder and induced folding
Q30365141	Assessing secondary structure assignment of protein structures by using pairwise sequence-alignment benchmarks.
Q90516508	Assessing the accuracy of contact predictions in CASP13
Q57600747	Assessing the acid-base and conformational properties of histidine residues in human prion protein (125-228) by means of pKa calculations and molecular dynamics simulations
Q47597353	Assessing the energy landscape of CAPRI targets by FunHunt
Q47909076	Assessing the reconstruction of macromolecular assemblies with toleranced models
Q51904487	Assessing the reliability of sequence similarities detected through hydrophobic cluster analysis
Q125345893	Assessing the utility of CASP14 models for molecular replacement
Q36672683	Assessment of 3D models for allergen research
Q28258469	Assessment of CAPRI predictions in rounds 3-5 shows progress in docking procedures
Q30352237	Assessment of CASP10 contact‐assisted predictions
Q30384592	Assessment of CASP11 contact-assisted predictions.
Q28274204	Assessment of CASP6 predictions for new and nearly new fold targets
Q28250579	Assessment of CASP7 predictions for template-based modeling targets
Q28250562	Assessment of CASP7 predictions in the high accuracy template-based modeling category
Q28250552	Assessment of CASP7 structure predictions for template free targets
Q35004666	Assessment of CASP8 structure predictions for template free targets
Q107868722	Assessment of Protein Model Structure Accuracy Estimation in CASP14: Old and New Challenges
Q34272407	Assessment of RAPTOR's linear programming approach in CAFASP3
Q57753457	Assessment of a protein fold recognition method that takes into account four physicochemical properties: side-chain packing, solvation, hydrogen-bonding, and local conformation
Q47613358	Assessment of blind predictions of protein-protein interactions: current status of docking methods
Q90380555	Assessment of chemical-crosslink-assisted protein structure modeling in CASP13
Q92908653	Assessment of chemical-crosslink-assisted protein structure modeling in CASP13
Q47628125	Assessment of comparative modeling in CASP2.
Q45944467	Assessment of contact predictions in CASP12: co-evolution and deep learning coming of age.
Q47299350	Assessment of data-assisted prediction by inclusion of crosslinking/mass-spectrometry and small angle X-ray scattering data in the 12th Critical Assessment of protein Structure Prediction experiment.
Q51963679	Assessment of disorder predictions in CASP6.
Q30363273	Assessment of disorder predictions in CASP7.
Q57998345	Assessment of disorder predictions in CASP8
Q30380197	Assessment of domain boundary predictions and the prediction of intramolecular contacts in CASP8.
Q30351465	Assessment of fold recognition predictions in CASP6.
Q43090923	Assessment of fully automated antibody homology modeling protocols in molecular operating environment
Q57208983	Assessment of global and local model quality in CASP8 using Pcons and ProQ
Q46130527	Assessment of hard target modeling in CASP12 reveals an emerging role of alignment-based contact prediction methods.
Q30336223	Assessment of homology-based predictions in CASP5.
Q30363176	Assessment of intramolecular contact predictions for CASP7.
Q30380200	Assessment of ligand binding residue predictions in CASP8
Q30356831	Assessment of ligand binding site predictions in CASP10
Q41782161	Assessment of ligand-binding residue predictions in CASP9.
Q46225966	Assessment of model accuracy estimations in CASP12.
Q54550923	Assessment of novel fold targets in CASP4: predictions of three-dimensional structures, secondary structures, and interresidue contacts.
Q30363275	Assessment of predictions in the model quality assessment category.
Q28274192	Assessment of predictions submitted for the CASP6 comparative modeling category
Q30363268	Assessment of predictions submitted for the CASP7 domain prediction category.
Q30363079	Assessment of predictions submitted for the CASP7 function prediction category.
Q44072765	Assessment of progress over the CASP experiments
Q46521126	Assessment of protein assembly prediction in CASP12.
Q92368472	Assessment of protein assembly prediction in CASP13
Q29048205	Assessment of protein disorder region predictions in CASP10
Q92767126	Assessment of protein model structure accuracy estimation in CASP13: Challenges in the era of deep learning
Q30360108	Assessment of protein side-chain conformation prediction methods in different residue environments.
Q30409206	Assessment of protein structure refinement in CASP9.
Q30386930	Assessment of refinement of template-based models in CASP11.
Q30408257	Assessment of template based protein structure predictions in CASP9.
Q30386933	Assessment of template-based modeling of protein structure in CASP11.
Q30356624	Assessment of template-based protein structure predictions in CASP10
Q30356925	Assessment of template-free modeling in CASP10 and ROLL.
Q77615096	Assessment of the CASP4 fold recognition category
Q29048204	Assessment of the assessment: evaluation of the model quality estimates in CASP10
Q45944463	Assessment of the model refinement category in CASP12.
Q30380207	Assessment of the protein-structure refinement category in CASP8
Q30980220	Assigning new GO annotations to protein data bank sequences by combining structure and sequence homology
Q30322703	Assigning secondary structure from protein coordinate data.
Q73798412	Assignment of enzyme substrate specificity by principal component analysis of aligned protein sequences: an experimental test using DNA glycosylase homologs
Q30358637	Assignment of polar states for protein amino acid residues using an interaction cluster decomposition algorithm and its application to high resolution protein structure modeling.
Q61758587	Assignment of the contribution of the tryptophan residues to the spectroscopic and functional properties of the ribotoxin alpha-sarcin
Q54702312	Assignment of the nucleotide binding sites and the mechanism of substrate inhibition of Escherichia coli adenylate kinase.
Q33241148	Association of calcineurin with mitochondrial proteins
Q46015642	Association of calmodulin and smooth muscle myosin light chain kinase: application of a label selection technique with trace acetylated calmodulin.
Q28291205	Associative mechanism for phosphoryl transfer: a molecular dynamics simulation of Escherichia coli adenylate kinase complexed with its substrates
Q85185882	Asymmetric amyloid fibril elongation: a new perspective on a symmetric world
Q50874939	Asymmetric inclusion by de novo designed proteins: fluorescence probe studies on amphiphilic alpha-helix bundles
Q28271287	At the dawn of the 21st century: Is dynamics the missing link for understanding enzyme catalysis?
Q71374330	Atomic and residue hydrophilicity in the context of folded protein structures
Q79210060	Atomic contact vectors in protein‐protein recognition
Q80353249	Atomic contacts in protein structures. A detailed analysis of atomic radii, packing, and overlaps
Q47715167	Atomic insight into the CD4 binding-induced conformational changes in HIV-1 gp120.
Q27648909	Atomic resolution (1.1 A) structure of the ribosome-inactivating protein PD-L4 from Phytolacca dioica L. leaves
Q27697263	Atomic resolution crystal structure of HV-BBI protease inhibitor from amphibian skin in complex with bovine trypsin
Q27643632	Atomic resolution crystal structures of HIV-1 protease and mutants V82A and I84V with saquinavir
Q27660254	Atomic resolution crystallography of a complex of triosephosphate isomerase with a reaction-intermediate analog: new insight in the proton transfer reaction mechanism
Q27640989	Atomic resolution structure of prokaryotic phospholipase A2: Analysis of internal motion and implication for a catalytic mechanism
Q27678807	Atomic structure of the nuclear pore complex targeting domain of a nup116 homologue from the yeast, Candida glabrata
Q51967602	Atomically detailed potentials to recognize native and approximate protein structures
Q45297035	Atomistic mechanisms of huntingtin N-terminal fragment insertion on a phospholipid bilayer revealed by molecular dynamics simulations
Q74449590	Atoms-in-molecules study of the genetically encoded amino acids. II. Computational study of molecular geometries
Q44515170	Atoms-in-molecules study of the genetically encoded amino acids. III. Bond and atomic properties and their correlations with experiment including mutation-induced changes in protein stability and genetic coding
Q79992379	Attempt to simplify the amino-acid sequence of photoactive yellow protein with a set of simple rules
Q34121578	Automatch: Target‐binding protein design and enzyme design by automatic pinpointing potential active sites in available protein scaffolds
Q30361881	Automated Aufbau of antibody structures from given sequences using Macromoltek's SmrtMolAntibody.
Q42005537	Automated antibody structure prediction using Accelrys tools: results and best practices
Q30329583	Automated assignment of SCOP and CATH protein structure classifications from FSSP scores.
Q46391824	Automated computation of low-energy pathways for complex rearrangements in proteins: application to the conformational switch of Ras p21.
Q46055675	Automated docking in crystallography: analysis of the substrates of aconitase
Q38311573	Automated docking of alpha-(1-->4)- and alpha-(1-->6)-linked glucosyl trisaccharides and maltopentaose into the soybean beta-amylase active site.
Q38345522	Automated docking of glucosyl disaccharides in the glucoamylase active site
Q38317891	Automated docking of maltose, 2-deoxymaltose, and maltotetraose into the soybean beta-amylase active site
Q38348797	Automated docking of monosaccharide substrates and analogues and methyl alpha-acarviosinide in the glucoamylase active site
Q34640538	Automated docking of substrates to proteins by simulated annealing
Q43825573	Automated docking to multiple target structures: incorporation of protein mobility and structural water heterogeneity in AutoDock
Q44379446	Automated generation of MCSS-derived pharmacophoric DOCK site points for searching multiconformation databases
Q42642389	Automated identification of binding sites for phosphorylated ligands in protein structures
Q30323114	Automated large scale evaluation of protein structure predictions.
Q30395997	Automated minimization of steric clashes in protein structures
Q52261420	Automated multiple analysis of protein structures: application to homology modeling of cytochromes P450.
Q47618994	Automated multiple structure alignment and detection of a common substructural motif
Q30336233	Automated prediction of CASP-5 structures using the Robetta server.
Q30351479	Automated prediction of domain boundaries in CASP6 targets using Ginzu and RosettaDOM.
Q46283837	Automated prediction of ligand-binding sites in proteins
Q28252646	Automated protein structure modeling in CASP9 by I‐TASSER pipeline combined with QUARK‐based ab initio folding and FG‐MD‐based structure refinement
Q39983192	Automated scaffold selection for enzyme design
Q28250590	Automated server predictions in CASP7
Q37348271	Automated site preparation in physics-based rescoring of receptor ligand complexes
Q39682349	Automated tertiary structure prediction with accurate local model quality assessment using the intfold‐ts method
Q30984863	Automated use of mutagenesis data in structure prediction
Q43561238	Automatic annotation of protein function based on family identification
Q57209027	Automatic consensus-based fold recognition using Pcons, ProQ, and Pmodeller
Q51986886	Automatic domain decomposition of proteins by a Gaussian Network Model
Q52335319	Automatic identification of discrete substates in proteins: singular value decomposition analysis of time-averaged crystallographic refinements
Q47597143	Automatic prediction of protein interactions with large scale motion
Q30358064	Automatic procedure for using models of proteins in molecular replacement.
Q47797377	Automatic structure prediction of oligomeric assemblies using Robetta in CASP12.
Q47307485	Automatic target selection for structural genomics on eukaryotes
Q51139343	Automating human intuition for protein design
Q30322332	Averaging interaction energies over homologs improves protein fold recognition in gapless threading.
Q46013258	Axial ligand replacement in horse heart cytochrome c by semisynthesis.
Q30437666	B. subtilis ykuD protein at 2.0 A resolution: insights into the structure and function of a novel, ubiquitous family of bacterial enzymes
Q44322003	BATMAS30: amino acid substitution matrix for alignment of bacterial transporters.
Q80934686	BAliBASE 3.0: latest developments of the multiple sequence alignment benchmark
Q30354487	BCL::Fold--protein topology determination from limited NMR restraints.
Q30373207	BCL::MP-fold: Membrane protein structure prediction guided by EPR restraints
Q36701877	BCL::SAXS: GPU accelerated Debye method for computation of small angle X-ray scattering profiles
Q34040043	BSP‐SLIM: A blind low‐resolution ligand‐protein docking approach using predicted protein structures
Q33384020	Backbone conformations and side chain flexibility of two somatostatin mimics investigated by molecular dynamics simulations
Q34389044	Backbone dependency further improves side chain prediction efficiency in the Energy-based Conformer Library (bEBL).
Q43256919	Backbone dynamics of TFE-induced native-like fold of region 4 of Escherichia coli RNA polymerase sigma70 subunit
Q73134460	Backbone dynamics of barstar: a (15)N NMR relaxation study
Q78675885	Backbone dynamics of the CC-chemokine eotaxin-2 and comparison among the eotaxin group chemokines
Q52035295	Backbone dynamics, fast folding, and secondary structure formation in helical proteins and peptides
Q73784255	Backbone entropy of loops as a measure of their flexibility: Application to a Ras protein simulated by molecular dynamics
Q80389891	Backbone-backbone geometry of tertiary contacts between alpha-helices
Q27743100	Bactericidal antibody recognition of a PorA epitope of Neisseria meningitidis: crystal structure of a Fab fragment in complex with a fluorescein-conjugated peptide
Q30397208	Balancing exploration and exploitation in population-based sampling improves fragment-based de novo protein structure prediction
Q30787844	Banding of NMR-derived methyl order parameters: implications for protein dynamics
Q27649937	Barley aldose reductase: structure, cofactor binding, and substrate recognition in the aldo/keto reductase 4C family
Q78854479	Basic interdomain boundary residues in calmodulin decrease calcium affinity of sites I and II by stabilizing helix-helix interactions
Q47388542	Bayesian estimation of NMR restraint potential and weight: a validation on a representative set of protein structures
Q30352859	Bayesian model aggregation for ensemble-based estimates of protein pKa values.
Q40744027	Bayesian probabilistic approach for predicting backbone structures in terms of protein blocks
Q51629036	Behavior of the ATP grasp domain of biotin carboxylase monomers and dimers studied using molecular dynamics simulations
Q30361172	Benchmarking of TASSER in the ab initio limit.
Q51952143	Benchmarking of dimeric threading and structure refinement
Q39273299	Benchmarking protein-protein interface predictions: why you should care about protein size
Q57851681	Benchmarking secondary structure prediction for fold recognition
Q30362845	Benchmarking template selection and model quality assessment for high-resolution comparative modeling.
Q40093904	Bending of the BST-2 coiled-coil during viral budding.
Q70618648	Beta VI turns in peptides and proteins: a model peptide mimicry
Q45028392	Beta-hairpin conformation of fibrillogenic peptides: structure and alpha-beta transition mechanism revealed by molecular dynamics simulations
Q27683632	Beta-lactamase of Bacillus licheniformis 749/C at 2 A resolution
Q35968690	Beta-sheet coil transitions in a simple polypeptide model
Q80353252	Beta-strand recombination in tricalbin evolution and the origin of synaptotagmin-like C2 domains
Q51099059	BetaVoid: molecular voids via beta-complexes and Voronoi diagrams
Q30156038	Beta‐barrel models of soluble amyloid beta oligomers and annular protofibrils
Q30429659	Better 1D predictions by experts with machines
Q30336265	Better prediction of sub-cellular localization by combining evolutionary and structural information.
Q33253189	Better prediction of the location of alpha-turns in proteins with support vector machine
Q57973959	Beyond Lumry-Eyring: An unexpected pattern of operational reversibility/irreversibility in protein denaturation
Q30376826	Beyond the Twilight Zone: automated prediction of structural properties of proteins by recursive neural networks and remote homology information.
Q30719266	Beyond the rotamer library: genetic algorithm combined with the disturbing mutation process for upbuilding protein side-chains
Q27700247	Bh3 induced conformational changes in Bcl-Xl revealed by crystal structure and comparative analysis
Q52078681	BiGGER: a new (soft) docking algorithm for predicting protein interactions
Q39692774	BiPPred: Combined sequence- and structure-based prediction of peptide binding to the Hsp70 chaperone BiP.
Q52053621	Bias-free separation of internal and overall motion of biomolecules
Q30410723	Bihelix: Towards de novo structure prediction of an ensemble of G‐protein coupled receptor conformations
Q81878003	Binding MOAD (Mother Of All Databases)
Q30157496	Binding and release of cholesterol in the Osh4 protein of yeast
Q90183701	Binding and structural studies of the complexes of type 1 ribosome inactivating protein from Momordica balsamina with uracil and uridine
Q81394699	Binding energy analysis for wild-type and Y181C mutant HIV-1 RT/8-Cl TIBO complex structures: quantum chemical calculations based on the ONIOM method
Q71374325	Binding geometry of alpha-helices that recognize DNA
Q35450396	Binding hotspots on K-ras: consensus ligand binding sites and other reactive regions from probe-based molecular dynamics analysis
Q46029368	Binding interactions of kistrin with platelet glycoprotein IIb-IIIa: analysis by site-directed mutagenesis.
Q41981433	Binding interface prediction by combining protein-protein docking results
Q53028079	Binding mode analysis of a major T3SS translocator protein PopB with its chaperone PcrH from Pseudomonas aeruginosa
Q43676072	Binding of AMP to two of the four subunits of pig kidney fructose-1,6-bisphosphatase induces the allosteric transition
Q51921200	Binding of antifusion peptides with HIVgp41 from molecular dynamics simulations: quantitative correlation with experiment
Q83053117	Binding of calcium is sensed structurally and dynamically throughout the second calcium-binding domain of the sodium/calcium exchanger
Q72668321	Binding of cyanide, cyanate, and thiocyanate to human carbonic anhydrase II
Q30344056	Binding of glutamine to glutamine-binding protein from Escherichia coli induces changes in protein structure and increases protein stability.
Q27658022	Binding of nitrogen-containing bisphosphonates (N-BPs) to the Trypanosoma cruzi farnesyl diphosphate synthase homodimer
Q34680971	Binding of nonsteroidal anti-inflammatory drugs to Abeta fibril
Q45194407	Binding of recombinant PrPc to human plasminogen: kinetic and thermodynamic study using a resonant mirror biosensor
Q52073334	Binding of small organic molecules to macromolecular targets: evaluation of conformational entropy changes
Q27649299	Binding of sulfonium-ion analogues of di-epi-swainsonine and 8-epi-lentiginosine to Drosophila Golgi alpha-mannosidase II: the role of water in inhibitor binding
Q50862492	Binding similarity network of ligand
Q34254661	Binding site multiplicity with fatty acid ligands: implications for the regulation of PKR kinase autophosphorylation with palmitate
Q51670398	Binding site prediction and improved scoring during flexible protein-protein docking with ATTRACT.
Q42675837	Binding site-based classification of coronaviral papain-like proteases
Q37083934	Binding specificity of SH2 domains: insight from free energy simulations
Q35070607	Binding to the open conformation of HIV-1 protease
Q30370399	BioGPS: navigating biological space to predict polypharmacology, off-targeting, and selectivity.
Q38288656	Biochemical characterization and structural insight into aliphatic β-amino acid adenylation enzymes IdnL1 and CmiS6.
Q46841052	Biological and functional relevance of CASP predictions.
Q30388103	Biological function derived from predicted structures in CASP11.
Q80752690	Biological implications of SNPs in signal peptide domains of human proteins
Q33318033	Biological roles of specific peptides in enzymes
Q81892387	Biologically enhanced sampling geometric docking and backbone flexibility treatment with multiconformational superposition
Q51149144	Biophysical characterization and structural determination of the potent cytotoxic Psathyrella asperospora lectin
Q56775080	Biophysical characterization of Vpu from HIV-1 suggests a channel-pore dualism
Q27649768	Biotinoyl domain of human acetyl-CoA carboxylase: Structural insights into the carboxyl transfer mechanism
Q77314214	Biphasic denaturation of human placental alkaline phosphatase in guanidinium chloride
Q44252311	BisANS binding to tubulin: isothermal titration calorimetry and the site-specific proteolysis reveal the GTP-induced structural stability of tubulin
Q90709301	Blind prediction of homo- and hetero-protein complexes: The CASP13-CAPRI experiment
Q36090741	Blind prediction of interfacial water positions in CAPRI
Q39251813	Blind prediction performance of RosettaAntibody 3.0: grafting, relaxation, kinematic loop modeling, and full CDR optimization.
Q30429651	Blind predictions of local protein structure in CASP2 targets using the I‐sites library
Q47584313	Blind predictions of protein interfaces by docking calculations in CAPRI
Q30385316	Blind testing of cross-linking/mass spectrometry hybrid methods in CASP11.
Q51501247	Blind, one‐eyed, or eagle‐eyed? pKa calculations during blind predictions with staphylococcal nuclease
Q92617098	Boosting phosphorylation site prediction with sequence feature-based machine learning
Q51591338	Both helical propensity and side-chain hydrophobicity at a partially exposed site in alpha-helix contribute to the thermodynamic stability of ubiquitin
Q57145042	Bridging between normal mode analysis and elastic network models
Q34434040	Bridging of anions by hydrogen bonds in nest motifs and its significance for Schellman loops and other larger motifs within proteins
Q30379050	Bridging of partially negative atoms by hydrogen bonds from main-chain NH groups in proteins: The crown motif.
Q58484057	Browsing gene banks for Fe2S2 ferredoxins and structural modeling of 88 plant-type sequences: An analysis of fold and function
Q30380943	BuildBeta--a system for automatically constructing beta sheets.
Q47826141	Building alternate protein structures using the elastic network model.
Q42661998	Building and assessing atomic models of proteins from structural templates: learning and benchmarks
Q44632652	Building interacting partner predictors using co-varying residue pairs between histidine kinase and response regulator pairs of 48 bacterial two-component systems
Q45969907	Building self-avoiding lattice models of proteins using a self-consistent field optimization.
Q52075239	Building-block approach for determining low-frequency normal modes of macromolecules
Q68494553	Bundles of amphipathic transmembrane alpha-helices as a structural motif for ion-conducting channel proteins: studies on sodium channels and acetylcholine receptors
Q87725977	Burial of nonpolar surface area and thermodynamic stabilization of globins as a function of chain elongation
Q77926208	C-terminal domain of gyrase A is predicted to have a beta-propeller structure
Q27653169	C-terminal tail derived from the neighboring subunit is critical for the activity of Thermoplasma acidophilum D-aldohexose dehydrogenase
Q27688045	C-terminal β-strand swapping in a consensus-derived fibronectin Type III scaffold
Q96233530	C1188D mutation abolishes specific recognition between MLL1-CXXC domain and CpG site by inducing conformational switch of flexible N- terminal
Q30420780	CAD-score: a new contact area difference-based function for evaluation of protein structural models.
Q57209048	CAFASP-1: Critical assessment of fully automated structure prediction methods
Q28145981	CAFASP-1: critical assessment of fully automated structure prediction methods
Q40661543	CAFASP2: the second critical assessment of fully automated structure prediction methods
Q79210041	CAFASP3 in the spotlight of EVA
Q57209029	CAFASP3: The third critical assessment of fully automated structure prediction methods
Q28258479	CAPRI rounds 3-5 reveal promising successes and future challenges for RosettaDock
Q84534732	CAPRI targets T29-T42: proving ground for new docking procedures
Q28208450	CAPRI: a Critical Assessment of PRedicted Interactions
Q30383453	CASP 11 target classification.
Q30353649	CASP prediction center infrastructure and evaluation measures in CASP10 and CASP ROLL.
Q30354839	CASP10 results compared to those of previous CASP experiments
Q30370695	CASP10-BCL::Fold efficiently samples topologies of large proteins.
Q30377096	CASP11 refinement experiments with ROSETTA.
Q30384245	CASP11 statistics and the prediction center evaluation system
Q91793346	CASP13 target classification into tertiary structure prediction categories
Q52281039	CASP2 experiences with docking flexible ligands using FlexX.
Q30329567	CASP2 knowledge-based approach to distant homology recognition and fold prediction in CASP4.
Q30429662	CASP2 molecular docking predictions with the LIGIN software
Q74252614	CASP2: Report on ab initio predictions
Q30794909	CASP3 comparative modeling evaluation
Q30336226	CASP5 assessment of fold recognition target predictions
Q42704736	CASP5 target classification
Q79209979	CASP5. Proceedings of the 5th Meeting on the Critical Assessment of Techniques for Protein Structure Prediction. 1-5 December 2002, Asilomar, California, USA
Q30351480	CASP6 assessment of contact prediction.
Q30351463	CASP6 data processing and automatic evaluation at the protein structure prediction center.
Q35000644	CASP8 results in context of previous experiments
Q30408132	CASP9 assessment of free modeling target predictions
Q42921761	CASP9 results compared to those of previous CASP experiments
Q30408141	CASP9 target classification
Q47715062	CHOP proteins into structural domain-like fragments
Q30365572	CLEMAPS: multiple alignment of protein structures based on conformational letters.
Q52434109	CLIX: A search algorithm for finding novel ligands capable of binding proteins of known three‐dimensional structure
Q51899748	CO escape from myoglobin with metadynamics simulations
Q57831887	COCO: A simple tool to enrich the representation of conformational variability in NMR structures
Q57975291	COMBINE analysis of the specificity of binding of Ras proteins to their effectors
Q30383444	COMSAT: Residue contact prediction of transmembrane proteins based on support vector machines and mixed integer linear programming.
Q30374675	CONFOLD: Residue-residue contact-guided ab initio protein folding.
Q84505249	CRK: an evolutionary approach for distinguishing biologically relevant interfaces from crystal contacts
Q79320573	Ca2+-dependent conformational changes in the neuronal Ca2+-sensor recoverin probed by the fluorescent dye Alexa647
Q104618312	Ca²⁺ as cofactor of the mitochondrial H⁺ -translocating F₁ F_O -ATP(hydrol)ase
Q36396802	CaMELS: In silico prediction of calmodulin binding proteins and their binding sites
Q80821117	Calcineurin B-like domains in the large regulatory alpha/beta subunits of phosphorylase kinase
Q84082968	Calcineurin regulatory subunit B is a unique calcium sensor that regulates calcineurin in both calcium-dependent and calcium-independent manner
Q43025211	Calcium binding to the purple membrane: A molecular dynamics study
Q78627298	Calcium binding to the transmembrane domain of the sarcoplasmic reticulum Ca2+-ATPase: insights from molecular modeling
Q79191077	Calcium-binding and temperature induced transitions in equine lysozyme: new insights from the pCa-temperature "phase diagrams"
Q70216501	Calcium-free calmodulin is a substrate of proteases from human immunodeficiency viruses 1 and 2
Q27731951	Calcium-independent subtilisin by design
Q44960722	Calculating proton uptake/release and binding free energy taking into account ionization and conformation changes induced by protein-inhibitor association: application to plasmepsin, cathepsin D and endothiapepsin-pepstatin complexes
Q30404964	Calculating three-dimensional changes in protein structure due to amino-acid substitutions: the variable region of immunoglobulins
Q52235998	Calculation of HyHel10-lysozyme binding free energy changes: Effect of ten point mutations
Q35846124	Calculation of pKa in proteins with the microenvironment modulated‐screened coulomb potential
Q52261413	Calculation of pathways for the conformational transition between the GTP‐ and GDP‐bound states of the Ha‐ras‐p21 protein: Calculations with explicit solvent simulations and comparison with calculations in vacuum
Q30323187	Calculation of protein conformation by global optimization of a potential energy function.
Q43825576	Calculation of protein ionization equilibria with conformational sampling: pKa of a model leucine zipper, GCN4 and barnase
Q30409635	Calculation of rate spectra from noisy time series data.
Q38567679	Calculation of the pitch of the alpha-helical coiled coil: an addendum
Q30403890	Calculation of the total electrostatic energy of a macromolecular system: solvation energies, binding energies, and conformational analysis
Q68701378	Calibration of effective van der Waals atomic contact radii for proteins and peptides
Q44546237	Calmodulin binding to alpha 1-purothionin: solution binding and modeling of the complex
Q82627891	Calmodulin signaling: analysis and prediction of a disorder-dependent molecular recognition
Q38333730	Camel single-domain antibody inhibits enzyme by mimicking carbohydrate substrate
Q43553705	Camps 2.0: exploring the sequence and structure space of prokaryotic, eukaryotic, and viral membrane proteins.
Q52082394	Can a pairwise contact potential stabilize native protein folds against decoys obtained by threading?
Q30360592	Can molecular dynamics simulations provide high-resolution refinement of protein structure?
Q46497570	Can one predict protein stability? An attempt to do so for residue 133 of T4 lysozyme using a combination of free energy derivatives, PROFEC, and free energy perturbation methods
Q30496929	Can self-inhibitory peptides be derived from the interfaces of globular protein-protein interactions?
Q47589178	Cancer-associated mutations are preferentially distributed in protein kinase functional sites
Q51930286	Cancer-related mutations in BRCA1-BRCT cause long-range structural changes in protein-protein binding sites: a molecular dynamics study
Q81193282	Candidate nsSNPs that can affect the functions and interactions of cell cycle proteins
Q41946585	Canonical structures of short CDR-L3 in antibodies
Q31115802	Capturing protein sequence-structure specificity using computational sequence design
Q42735601	Capturing the energetics of water insertion in biological systems: The water flooding approach
Q27695696	Carbohydrate binding module recognition of xyloglucan defined by polar contacts with branching xyloses and CH-Π interactions
Q91742229	Cardosin A endocytosis mediated by integrin leads to lysosome leakage and apoptosis of epithelial cells
Q47256063	Cartilage acidic protein 1, a new member of the beta-propeller protein family with amyloid propensity
Q70726296	Catalysis by dienelactone hydrolase: a variation on the protease mechanism
Q92995874	Catalytic triad heterogeneity in S51 peptidase family: Structural basis for functional variability
Q80011300	Cation-aromatic database
Q45279404	Cation-pi interactions in protein-protein interfaces
Q33754213	Cation-π interactions of methylated ammonium ions: a quantum mechanical study
Q87217903	Cation-π, amino-π, π-π, and H-bond interactions stabilize antigen-antibody interfaces
Q48189831	Causality, transfer entropy, and allosteric communication landscapes in proteins with harmonic interactions
Q37069889	Cell cycle kinases predicted from conserved biophysical properties
Q33947335	Cell surface receptors and their ligands: in vitro analysis of CD6-CD166 interactions
Q52251886	Chain conformation in polyretropeptides III: Design of a 310 helix using α,α-dialkylated amino acids and retropeptide bonds
Q58037861	Chain length is the main determinant of the folding rate for proteins with three-state folding kinetics
Q93026588	Challenges and opportunities of automated protein-protein docking: HDOCK server vs human predictions in CAPRI Rounds 38-46
Q33494609	Challenging a paradigm: theoretical calculations of the protonation state of the Cys25-His159 catalytic diad in free papain
Q27680838	Challenging the state of the art in protein structure prediction: Highlights of experimental target structures for the 10th Critical Assessment of Techniques for Protein Structure Prediction Experiment CASP10
Q45934507	Change in protein flexibility upon complex formation: analysis of Ras-Raf using molecular dynamics and a molecular framework approach.
Q47810386	Change of thermal stability of colicin E7 triggered by acidic pH suggests the existence of unfolded intermediate during the membrane-translocation phase
Q68666381	Changes in secondary structure follow the dissociation of human insulin hexamers: a circular dichroism study
Q46313885	Changes in the electron density of the cofactor NADPH on binding to E. coli dihydrofolate reductase
Q52251898	Chaos in protein dynamics
Q46296756	Chaperone action of a versatile small heat shock protein from Methanococcoides burtonii, a cold adapted archaeon
Q47589403	Chaperone-client interactions between Hsp21 and client proteins monitored in solution by small angle X-ray scattering and captured by crosslinking mass spectrometry.
Q91231457	Chaperone-like activity of the N-terminal region of a human small heat shock protein and chaperone-functionalized nanoparticles
Q79624974	Chaperone-mediated inhibition of tubulin self-assembly
Q51924709	Characteristic amino acid combinations in olfactory G protein-coupled receptors
Q42645617	Characterization and autoprocessing of precursor and mature forms of human immunodeficiency virus type 1 (HIV 1) protease purified from Escherichia coli
Q57088189	Characterization and functional properties of the extracellular coelomic hemoglobins from the deep-sea, hydrothermal vent scaleworm Branchipolynoe symmytilida
Q46982720	Characterization and structural modeling of a novel thermostable glycine oxidase from Geobacillus kaustophilus HTA426.
Q42036089	Characterization and tissue-specific expression of two lepidopteran farnesyl diphosphate synthase homologs: implications for the biosynthesis of ethyl-substituted juvenile hormones
Q47866998	Characterization of Arabidopsis thaliana stellacyanin: a comparison with umecyanin
Q68188218	Characterization of HIV-1 p24 self-association using analytical affinity chromatography
Q98198405	Characterization of Left-handed beta Helix-domains, and identification and functional annotation of proteins containing such domains
Q44947535	Characterization of Lys-698-to-Met substitution in human plasminogen catalytic domain
Q30010236	Characterization of PDZ domain‐peptide interaction interface based on energetic patterns
Q40376423	Characterization of Salmonella typhi OmpC and OmpF porins engineered with HIV-gp41 epitope on the surface loops
Q27644271	Characterization of Salmonella typhimurium YegS, a putative lipid kinase homologous to eukaryotic sphingosine and diacylglycerol kinases
Q43021929	Characterization of a corrinoid protein involved in the C1 metabolism of strict anaerobic bacterium Moorella thermoacetica
Q27653535	Characterization of a diagnostic Fab fragment binding trimeric Lewis X
Q45865791	Characterization of a putative calcium-binding site in tobacco mosaic virus
Q46548593	Characterization of a sHsp of Schizosaccharomyces pombe, SpHsp15.8, and the implication of its functional mechanism by comparison with another sHsp, SpHsp16.0.
Q54768947	Characterization of a slow folding reaction for the alpha subunit of tryptophan synthase.
Q43593727	Characterization of a thrombomodulin binding site on protein C and its comparison to an activated protein C binding site for factor Va.
Q53393870	Characterization of an alternative low energy fold for bovine α‐lactalbumin formed by disulfide bond shuffling
Q47771231	Characterization of cancer-linked BRCA1-BRCT missense variants and their interaction with phosphoprotein targets
Q31138279	Characterization of carbonic anhydrases from Riftia pachyptila, a symbiotic invertebrate from deep-sea hydrothermal vents
Q71660325	Characterization of crystals of Penicillium purpurogenum acetyl xylan esterase from high-resolution x-ray diffraction
Q57979651	Characterization of crystals of the thermostable DNA polymerase I fromthermus aquaticus
Q46261187	Characterization of cysteine thiol modifications based on protein microenvironments and local secondary structures
Q40314632	Characterization of de novo four-helix bundles by molecular dynamics simulations
Q80068376	Characterization of interfacial solvent in protein complexes and contribution of wet spots to the interface description
Q74614435	Characterization of internal motions of Escherichia coli ribonuclease H by Monte Carlo simulation
Q43256880	Characterization of intrinsically disordered proteins with electrospray ionization mass spectrometry: conformational heterogeneity of alpha-synuclein
Q30365524	Characterization of local geometry of protein surfaces with the visibility criterion.
Q30320157	Characterization of peptides resulting from digestion of human skin elastin with elastase.
Q92309401	Characterization of perdeuterated high-potential iron-sulfur protein with high-resolution X-ray crystallography
Q70604305	Characterization of proline-containing alpha-helix (helix F model of bacteriorhodopsin) by molecular dynamics studies
Q81489824	Characterization of protein dynamics from residual dipolar couplings using the three dimensional Gaussian axial fluctuation model
Q46129874	Characterization of receptors with a new negative image: Use in molecular docking and lead optimization
Q31149794	Characterization of sequence variability in nucleosome core histone folds.
Q51521576	Characterization of the AXH domain of Ataxin-1 using enhanced sampling and functional mode analysis.
Q47422752	Characterization of the active site of DNA polymerase β by molecular dynamics and quantum chemical calculation
Q51079352	Characterization of the active site of group B streptococcal hyaluronan lyase
Q73798420	Characterization of the active site of group B streptococcal hyaluronan lyase
Q48007276	Characterization of the amino acid contribution to the folding degree of proteins
Q36778462	Characterization of the backbone dynamics of an anti-digoxin antibody VL domain by inverse detected 1H-15N NMR: comparisons with X-ray data for the Fab.
Q30354980	Characterization of the backbone geometry of protein native state structures.
Q30962824	Characterization of the conformational space of a triple-stranded beta-sheet forming peptide with molecular dynamics simulations
Q30976908	Characterization of the denaturation of human alpha-lactalbumin in urea by molecular dynamics simulations
Q29048196	Characterization of the differences in the cyclopiazonic acid binding mode to mammalian and P. Falciparum Ca2+ pumps: a computational study
Q27687987	Characterization of the divalent metal binding site of bacterial polysaccharide deacetylase using crystallography and quantum chemical calculations
Q27640569	Characterization of the electrophile binding site and substrate binding mode of the 26-kDa glutathione S-transferase from Schistosoma japonicum
Q41710730	Characterization of the flexibility of the peripheral stalk of prokaryotic rotary A-ATPases by atomistic simulations
Q77669594	Characterization of the folding pathway of recombinant human macrophage-colony stimulating-factor beta (rhM-CSF beta) by bis-cysteinyl modification and mass spectrometry
Q39627714	Characterization of the homodimerization interface and functional hotspots of the CXCR4 chemokine receptor
Q43825905	Characterization of the impact of alternative splicing on protein dynamics: the cases of glutathione S-transferase and ectodysplasin-A isoforms
Q45713086	Characterization of the near native conformational states of the SAM domain of Ste11 protein by NMR spectroscopy
Q30157626	Characterization of the outer membrane protein OprF of Pseudomonas aeruginosa in a lipopolysaccharide membrane by computer simulation
Q57976889	Characterization of the residual structure in the unfolded state of the Δ131Δ fragment of staphylococcal nuclease
Q45036370	Characterization of the structure and catalytic activity of Legionella pneumophila VipF.
Q54632303	Characterization of two crystal forms of Clostridium thermocellum endoglucanase CelC.
Q91137986	Characterizing molecular flexibility by combining least root mean square deviation measures
Q30365845	Characterizing of functional human coding RNA editing from evolutionary, structural, and dynamic perspectives.
Q45765685	Characterizing the binding of annexin V to a lipid bilayer using molecular dynamics simulations
Q51317035	Characterizing the conformational ensemble of monomeric polyglutamine.
Q51342935	Characterizing the morphology of protein binding patches.
Q73844969	Charge centers and formation of the protein folding core
Q43885118	Charged single alpha-helix: a versatile protein structural motif
Q38408842	Chemical compound navigator: a web-based chem-BLAST, chemical taxonomy-based search engine for browsing compounds
Q71543071	Chemical cross-linking between lysine groups in vimentin oligomers is dependent on local peptide conformations
Q69569349	Chemical modification of the RTEM-1 thiol beta-lactamase by thiol-selective reagents: evidence for activation of the primary nucleophile of the beta-lactamase active site by adjacent functional groups
Q60129856	Chemical synthesis of mouse cripto CFC variants
Q82462297	Chemometric tools for classification and elucidation of protein secondary structure from infrared and circular dichroism spectroscopic measurements
Q51379039	Choice of synonymous codons associated with protein folding
Q44352138	Cholesterol-β1 AR interaction versus cholesterol-β2 AR interaction
Q47561394	Choosing non-redundant representative subsets of protein sequence data sets using submodular optimization
Q70830930	Circular dichroism of the parallel beta helical proteins pectate lyase C and E
Q57753147	Circular permutants in β-glucosidases (family 3) within a predicted double-domain topology that includes a (β/α)8-barrel
Q21045416	Circular permuted proteins in the universe of protein folds
Q47258354	Cis/trans isomerization in HIV-1 capsid protein catalyzed by cyclophilin A: insights from computational and theoretical studies
Q96340486	Citius, Altius, Fortius
Q37083960	Clarifying allosteric control of flap conformations in the 1TW7 crystal structure of HIV-1 protease.
Q75209215	Class-specific correlations between protein folding rate, structure-derived, and sequence-derived descriptors
Q43825564	Classical molecular interaction potentials: improved setup procedure in molecular dynamics simulations of proteins.
Q27935991	Classification and functional annotation of eukaryotic protein kinases
Q47258295	Classification of common functional loops of kinase super-families
Q80678271	Classification of conformational stability of protein mutants from 3D pseudo-folding graph representation of protein sequences using support vector machines
Q51421512	Classification of protein complexes based on docking difficulty
Q52133653	Classification of protein sequences by homology modeling and quantitative analysis of electrostatic similarity
Q43947457	Classification of proteins based on the properties of the ligand-binding site: the case of adenine-binding proteins
Q30809775	Classification of the caspase-hemoglobinase fold: detection of new families and implications for the origin of the eukaryotic separins
Q83098493	Classification of transporters using efficient radial basis function networks with position-specific scoring matrices and biochemical properties
Q27648694	Classifying protein kinase structures guides use of ligand-selectivity profiles to predict inactive conformations: structure of lck/imatinib complex
Q47718245	Cloning and characterization of a caesalpinoid (Chamaecrista fasciculata) hemoglobin: the structural transition from a nonsymbiotic hemoglobin to a leghemoglobin.
Q60602325	Cloning and expression of the uracil-DNA glycosylase inhibitor (UGI) from bacteriophage PBS-1 and crystallization of a uracil-DNA glycosylase-UGI complex
Q36448470	Cloning, expression, and nucleotide sequence of livR, the repressor for high-affinity branched-chain amino acid transport in Escherichia coli
Q90107881	ClusPro in rounds 38 to 45 of CAPRI: Toward combining template-based methods with free docking
Q51905726	ClusPro: performance in CAPRI rounds 6-11 and the new server
Q42635958	Cluster conservation as a novel tool for studying protein-protein interactions evolution
Q30350530	Clustering algorithms for identifying core atom sets and for assessing the precision of protein structure ensembles.
Q30374983	Clustering and visualizing similarity networks of membrane proteins.
Q51384741	Clustering biomolecular complexes by residue contacts similarity
Q57752503	Clustering of multi-domain protein sequences
Q46978001	Clustering of null mutations in the EcoRI endonuclease
Q50862494	Clustering orthologous proteins across phylogenetically distant species
Q30168356	Clusters in alpha/beta barrel proteins: implications for protein structure, function, and folding: a graph theoretical approach
Q40860270	Co-evolutionary analysis implies auxiliary functions of HSP110 in Plasmodium falciparum
Q33219608	Co-translational myristoylation alters the quaternary structure of HIV-1 Nef in solution
Q46111975	Coarse grain lipid-protein molecular interactions and diffusion with MsbA flippase
Q30424079	Coarse- and fine-grained models for proteins: evaluation by decoy discrimination
Q44249508	Coarse-grained and all-atom modeling of structural states and transitions in hemoglobin
Q91563817	Coarse-grained and atomic resolution biomolecular docking with the ATTRACT approach
Q51888469	Coarse-grained dynamics of the receiver domain of NtrC: fluctuations, correlations and implications for allosteric cooperativity.
Q87366219	Coarse-grained modeling of the intrinsically disordered protein Histatin 5 in solution: Monte Carlo simulations in combination with SAXS
Q47625877	Coarse-grained simulations of conformational dynamics of proteins: Application to apomyoglobin
Q51367033	Coarse-grained simulations of proton-dependent conformational changes in lactose permease
Q84136480	Coarse‐grained modeling of conformational transitions underlying the processive stepping of myosin V dimer along filamentous actin
Q58360796	Cocrystallization of Lysyl-tRNA synthetase fromThermus thermophilus with its cognate tRNAlys and withEscherichia coli tRNAlys
Q83192173	Codep: maximizing co-evolutionary interdependencies to discover interacting proteins
Q33373404	Coevolution in defining the functional specificity
Q38876977	Coevolutionary constraints in the sequence-space of macromolecular complexes reflect their self-assembly pathways
Q42684108	Cofactor assisted gating mechanism in the active site of NADH oxidase from Thermus thermophilus
Q42625526	Cofactor-binding sites in proteins of deviating sequence: comparative analysis and clustering in torsion angle, cavity, and fold space
Q39328444	Cofactors-loaded quaternary structure of lysine-specific demethylase 5C (KDM5C) protein: Computational model
Q51112347	Cofactory: sequence-based prediction of cofactor specificity of Rossmann folds
Q27656244	Cohesin diversity revealed by the crystal structure of the anchoring cohesin from Ruminococcus flavefaciens
Q73594398	Cohesin-dockerin recognition in cellulosome assembly: experiment versus hypothesis
Q90307969	Coil conversion to β-strand induced by dimerization
Q46666901	Coiled-coil length: Size does matter.
Q52871341	Coiled-coil stutter and link segments in keratin and other intermediate filament molecules: a computer modeling study
Q27730353	Cold adaption of enzymes: structural comparison between salmon and bovine trypsins
Q73521271	Cold denaturation of alpha-lactalbumin
Q57956349	Cold unfolding of β-hairpins: A molecular-level rationalization
Q41834158	Collective dynamics of the ribosomal tunnel revealed by elastic network modeling
Q72335565	Collective motions in proteins investigated by X-ray diffuse scattering
Q52465150	Collective motions in proteins: A covariance analysis of atomic fluctuations in molecular dynamics and normal mode simulations
Q51794147	Combination of scoring functions improves discrimination in protein-protein docking
Q44404796	Combined QM/MM mechanistic study of the acylation process in furin complexed with the H5N1 avian influenza virus hemagglutinin's cleavage site
Q51775539	Combined computational and biochemical study reveals the importance of electrostatic interactions between the "pH sensor" and the cation binding site of the sodium/proton antiporter NhaA of Escherichia coli
Q41642027	Combined computational and experimental analysis of a complex of ribonuclease III and the regulatory macrodomain protein, YmdB
Q33854315	Combined computational design of a zinc-binding site and a protein-protein interaction: one open zinc coordination site was not a robust hotspot for de novo ubiquitin binding
Q30403472	Combined procedure of distance geometry and restrained molecular dynamics techniques for protein structure determination from nuclear magnetic resonance data: application to the DNA binding domain of lac repressor from Escherichia coli
Q27664843	Combined use of computational chemistry, NMR screening, and X-ray crystallography for identification and characterization of fluorophilic protein environments
Q51082691	Combining ancestral sequence reconstruction with protein design to identify an interface hotspot in a key metabolic enzyme complex
Q84843927	Combining coarse‐grained nonbonded and atomistic bonded interactions for protein modeling
Q27657212	Combining crystallography and molecular dynamics: the case of Schistosoma mansoni phospholipid glutathione peroxidase
Q30342425	Combining evolutionary and structural information for local protein structure prediction.
Q29614392	Combining evolutionary information and neural networks to predict protein secondary structure
Q41462734	Combining features in a graphical model to predict protein binding sites
Q38405905	Combining functional and topological properties to identify core modules in protein interaction networks.
Q46394449	Combining interface core and whole interface descriptors in postscan processing of protein-protein docking models
Q30336231	Combining local-structure, fold-recognition, and new fold methods for protein structure prediction.
Q27638993	Combining mutations in HIV-1 protease to understand mechanisms of resistance
Q28239844	Combining prediction of secondary structure and solvent accessibility in proteins
Q40636300	Combining the GOR V algorithm with evolutionary information for protein secondary structure prediction from amino acid sequence
Q29619067	Combining the polymerase incomplete primer extension method for cloning and mutagenesis with microscreening to accelerate structural genomics efforts
Q54535231	Coming to peace with protein complexes? 5th CAPRI evaluation meeting, April 17-19th 2013--Utrecht.
Q73798390	Comment on "a fast and simple method to calculate protonation states in proteins"
Q79838664	Comment on Probe-dependent and nonexponential relaxation kinetics: unreliable signatures of downhill protein folding
Q44018178	Comment on ion transit pathways and gating in ClC chloride channels
Q57956455	Comment on “Phenomenological similarities between protein denaturation and small-molecule dissolution: Insights into the mechanism driving the thermal resistance of globular proteins” (Proteins 2004;54:323-332)
Q58008891	Comment on: “Energy landscape of a small peptide revealed by dihedral angle principal component analysis”
Q73427984	Comment to Daura, X., et al., Proteins 25:89-103, 1996
Q44864924	Commentary on: "Assembly of a tetrameric alpha-helical bundle: computer simulations on an intermediate-resolution protein model" [Proteins 2001;44:376-391].
Q38322076	Common binding site for disialyllactose and tri-peptide in C-fragment of tetanus neurotoxin
Q27646624	Common conformational changes in flavodoxins induced by FMN and anion binding: the structure of Helicobacter pylori apoflavodoxin
Q47637017	Common features of the conformations of antigen-binding loops in immunoglobulins and application to modeling loop conformations
Q34989642	Common functionally important motions of the nucleotide-binding domain of Hsp70
Q94529184	Common mechanism of thermostability in small α- and β-proteins studied by molecular dynamics
Q30365144	Common occurrence of internal repeat symmetry in membrane proteins.
Q77386261	Common structural elements in the architecture of the cofactor-binding domains in unrelated families of pyridoxal phosphate-dependent enzymes
Q34083289	Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions
Q57267827	Compact conformations of α-synuclein induced by alcohols and copper
Q46753799	Compact dimension of denatured states of staphylococcal nuclease
Q43018619	Compact reduced thioredoxin structure from the thermophilic bacteria Thermus thermophilus
Q27622761	Comparative X-ray analysis of the un-liganded fosfomycin-target murA
Q30388080	Comparative analyses of quaternary arrangements in homo-oligomeric proteins in superfamilies: Functional implications
Q81171039	Comparative analysis of HIV-1 Tat variants
Q42662784	Comparative analysis of amino acid distributions in integral membrane proteins from 107 genomes
Q52641027	Comparative analysis of nanobody sequence and structure data.
Q51099046	Comparative analysis of sequence covariation methods to mine evolutionary hubs: examples from selected GPCR families
Q44755455	Comparative analysis of structural properties of the C-type-lectin-like domain (CTLD).
Q68137855	Comparative analysis of the beta transducin family with identification of several new members including PWP1, a nonessential gene of Saccharomyces cerevisiae that is divergently transcribed from NMT1
Q68051379	Comparative analysis of the sequences and structures of HIV-1 and HIV-2 proteases
Q43273730	Comparative binding energy analysis for binding affinity and target selectivity prediction
Q92477078	Comparative dynamics of tropomyosin in vertebrates and invertebrates
Q36144310	Comparative electrostatic analysis of adenylyl cyclase for isoform dependent regulation properties
Q92454884	Comparative electrostatic analysis of adenylyl cyclase for isoform dependent regulation properties
Q33206310	Comparative evaluation of eight docking tools for docking and virtual screening accuracy
Q30159802	Comparative model of EutB from coenzyme B12-dependent ethanolamine ammonia-lyase reveals a beta8alpha8, TIM-barrel fold and radical catalytic site structural features
Q35948872	Comparative modeling and protein‐like features of hydrophobic–polar models on a two‐dimensional lattice
Q30336362	Comparative modeling in CASP5: progress is evident, but alignment errors remain a significant hindrance.
Q30351468	Comparative modeling in CASP6 using consensus approach to template selection, sequence-structure alignment, and structure assessment.
Q43524110	Comparative modeling methods: application to the family of the mammalian serine proteases
Q57931644	Comparative modeling of CASP3 targets using PSI-BLAST and SCWRL
Q30794937	Comparative modeling of CASP3 targets using PSI-BLAST and SCWRL.
Q30329566	Comparative modeling of CASP4 target proteins: combining results of sequence search with three-dimensional structure assessment.
Q45818968	Comparative modeling of human NSF reveals a possible binding mode of GABARAP and GATE-16.
Q44899548	Comparative modeling of mammalian aspartate transcarbamylase
Q40914759	Comparative modeling of the three-dimensional structure of the calmodulin-related TCH2 protein from Arabidopsis
Q57752842	Comparative modeling of the three-dimensional structures of family 3 glycoside hydrolases
Q73798371	Comparative modeling studies of the calmodulin-like domain of calcium-dependent protein kinase from soybean
Q53861662	Comparative molecular dynamics simulations of HIV-1 integrase and the T66I/M154I mutant: binding modes and drug resistance to a diketo acid inhibitor.
Q40105003	Comparative molecular dynamics simulations of histone deacetylase-like protein: binding modes and free energy analysis to hydroxamic acid inhibitors
Q42671024	Comparative molecular dynamics--similar folds and similar motions?
Q28293707	Comparative molecular model building of two serine proteinases from cytotoxic T lymphocytes
Q49162124	Comparative molecular modeling and crystallization of P-30 protein: a novel antitumor protein of Rana pipiens oocytes and early embryos
Q30164931	Comparative properties of a three-dimensional model of Plasmodium falciparum ornithine decarboxylase.
Q112582357	Comparative protein structure network analysis on 3CL^pro from SARS-CoV-1 and SARS-CoV-2
Q54238877	Comparative proteome analysis reveals pathogen specific outer membrane proteins of Leptospira
Q43018776	Comparative sequence and structure analysis reveal features of cold adaptation of an enzyme in the thermolysin family
Q30160304	Comparative structural analysis of TonB-dependent outer membrane transporters: implications for the transport cycle
Q51130506	Comparative structural analysis of a novel glutathioneS-transferase (ATU5508) from Agrobacterium tumefaciens at 2.0 A resolution
Q43030179	Comparative structural analysis of psychrophilic and meso- and thermophilic enzymes
Q42718380	Comparative structural analysis of the binding domain of follicle stimulating hormone receptor
Q81521844	Comparative structure-function analysis of cytolethal distending toxins
Q48045765	Comparative studies of the catalytic mechanisms of two chorismatases: CH-fkbo and CH-Hyg5.
Q93059675	Comparative studies on ion-pair energetic, distribution among three domains of life: Archaea, eubacteria, and eukarya
Q91294636	Comparative study of the effect of disease causing and benign mutations in position Q92 on cholesterol binding by the NPC1 n-terminal domain
Q30558517	Comparing aminoglycoside binding sites in bacterial ribosomal RNA and aminoglycoside modifying enzymes
Q30352610	Comparing atomistic simulation data with the NMR experiment: how much can NOEs actually tell us?
Q46877421	Comparing folding codes for proteins and polymers
Q51239716	Comparing programs for rigid-body multiple structural superposition of proteins
Q36152993	Comparing protein-ligand docking programs is difficult.
Q52545253	Comparing short protein substructures by a method based on backbone torsion angles
Q50087493	Comparing side chain packing in soluble proteins, protein-protein interfaces, and transmembrane proteins
Q45327298	Comparing the folding free-energy landscapes of Abeta42 variants with different aggregation properties
Q51041059	Comparison between computational alanine scanning and per-residue binding free energy decomposition for protein-protein association using MM-GBSA: application to the TCR-p-MHC complex
Q54735679	Comparison of CD spectra in the aromatic region on a series of variant proteins substituted at a unique position of tryptophan synthase alpha-subunit.
Q30368397	Comparison of Composer and ORCHESTRAR.
Q43475406	Comparison of DNA binding across protein superfamilies.
Q47433501	Comparison of NMR and crystal structures of membrane proteins and computational refinement to improve model quality
Q92174616	Comparison of Rosetta flexible-backbone computational protein design methods on binding interactions
Q58037841	Comparison of X-ray and NMR structures: Is there a systematic difference in residue contacts between X-ray- and NMR-resolved protein structures?
Q44296010	Comparison of a QM/MM force field and molecular mechanics force fields in simulations of alanine and glycine "dipeptides" (Ace-Ala-Nme and Ace-Gly-Nme) in water in relation to the problem of modeling the unfolded peptide backbone in solution
Q71565956	Comparison of an antibody model with an X-ray structure: the variable fragment of BR96
Q60214155	Comparison of backbone dynamics of monomeric and domain-swapped stefin A
Q58201930	Comparison of cell-based and cell-free protocols for producing target proteins from the Arabidopsis thaliana genome for structural studies
Q27643815	Comparison of cytochromes b5 from insects and vertebrates
Q73845036	Comparison of different schemes to treat long-range electrostatic interactions in molecular dynamics simulations of a protein crystal
Q57127575	Comparison of end-point continuum-solvation methods for the calculation of protein-ligand binding free energies
Q71565961	Comparison of low oxidoreduction potential cytochrome c553 from Desulfovibrio vulgaris with the class I cytochrome c family
Q68085492	Comparison of model and nuclear magnetic resonance structures for the human inflammatory protein C5a
Q27861040	Comparison of multiple Amber force fields and development of improved protein backbone parameters
Q30329575	Comparison of performance in successive CASP experiments.
Q56144901	Comparison of protein active site structures for functional annotation of proteins and drug design
Q30331167	Comparison of sequence and structure alignments for protein domains.
Q30351001	Comparison of sequence and structure-based datasets for nonredundant structural data mining.
Q32063335	Comparison of solution and crystal structures of maize nonspecific lipid transfer protein: A model for a potential in vivo lipid carrier protein
Q42939604	Comparison of structure-based and threading-based approaches to protein functional annotation
Q27663391	Comparison of the crystal structure of bacteriophage T4 lysozyme at low, medium, and high ionic strengths
Q68033364	Comparison of the dynamics of the membrane-bound form of fd coat protein in micelles and in bilayers by solution and solid-state nitrogen-15 nuclear magnetic resonance spectroscopy
Q71763600	Comparison of the effects of hydrophobicity, amphiphilicity, and alpha-helicity on the activities of antimicrobial peptides
Q51897349	Comparison of the efficiency of evolutionary change-based and side chain orientation-based fold recognition potentials
Q46251102	Comparison of the folding mechanism of highly homologous proteins in the lipid-binding protein family.
Q30195472	Comparison of the hemocyanin beta-barrel with other Greek key beta-barrels: possible importance of the "beta-zipper" in protein structure and folding
Q41209700	Comparison of the structures of globins and phycocyanins: evidence for evolutionary relationship
Q46794596	Comparison of the three-dimensional structure of two human rhinoviruses (HRV2 and HRV14).
Q28241164	Comparison of the transition state ensembles for folding of Im7 and Im9 determined using all-atom molecular dynamics simulations with phi value restraints
Q52074689	Comparison of two optimization methods to derive energy parameters for protein folding: perceptron and Z score
Q27648960	Comparison of vertebrate and invertebrate CLIC proteins: the crystal structures of Caenorhabditis elegans EXC-4 and Drosophila melanogaster DmCLIC
Q42630672	Comparisons of experimental and computed protein anisotropic temperature factors
Q30429635	Competitive assessment of protein fold recognition and alignment accuracy
Q51929128	Complementarity of hydrophobic properties in ATP-protein binding: a new criterion to rank docking solutions
Q47311209	Complementarity of stability patches at the interfaces of protein complexes: Implication for the structural organization of energetic hot spots.
Q41158742	Complete characterization of the mutation landscape reveals the effect on amylin stability and amyloidogenicity
Q28220809	Completion and refinement of 3-D homology models with restricted molecular dynamics: application to targets 47, 58, and 111 in the CASP modeling competition and posterior analysis
Q46853494	Complex assembly mechanism and an RNA-binding mode of the human p14-SF3b155 spliceosomal protein complex identified by NMR solution structure and functional analyses
Q47258345	Complex folding pathways in a simple beta-hairpin
Q51556411	Complex formation dynamics of native and mutated pyrin's B30.2 domain with caspase-1.
Q46010779	Complexes of HIV-1 integrase with HAT proteins: multiscale models, dynamics, and hypotheses on allosteric sites of inhibition.
Q51931326	Complexity of free energy landscapes of peptides revealed by nonlinear principal component analysis
Q50671762	Component D of chicken hemoglobin and the hemoglobin of the embryonic Tammar wallaby (Macropus eugenii) self-associate upon deoxygenation: Effect on oxygen binding
Q53168946	Comprehensive analysis of motions in molecular dynamics trajectories of the actin capping protein and its inhibitor complexes
Q46794984	Comprehensive analysis of the helix-X-helix motif in soluble proteins
Q30367296	Comprehensive description of protein structures using protein folding shape code.
Q52344954	Comprehensive mapping of cystic fibrosis mutations to CFTR protein identifies mutation clusters and molecular docking predicts corrector binding site.
Q47822299	Comprehensive secondary-structure analysis of disulfide variants of lysozyme by synchrotron-radiation vacuum-ultraviolet circular dichroism.
Q58024639	Comprehensive statistical analysis of residues interaction specificity at protein-protein interfaces
Q43825551	Computation and mutagenesis suggest a right‐handed structure for the synaptobrevin transmembrane dimer
Q45966452	Computation of conformational entropy from protein sequences using the machine-learning method--application to the study of the relationship between structural conservation and local structural stability.
Q43825546	Computational 3‐D modeling and site‐directed mutation of an antibody that binds Neu2en5Ac, a transition state analogue of a sialic acid
Q58112055	Computational Investigation of the Conformational Dynamics in Tom20-Mitochondrial Presequence Tethered Complexes
Q42643262	Computational active site analysis of molecular pathways to improve functional classification of enzymes
Q34056558	Computational alanine scanning with linear scaling semiempirical quantum mechanical methods
Q34689386	Computational analysis of folding and mutation properties of C5 domain of myosin binding protein C.
Q40431535	Computational analysis of molecular basis of 1:1 interactions of NRG-1beta wild-type and variants with ErbB3 and ErbB4.
Q130681476	Computational analysis of propeptide‐containing proteins and prediction of their post‐cleavage conformation changes
Q30385837	Computational analysis of the CB1 carboxyl-terminus in the receptor-G protein complex
Q57227211	Computational analysis of the S. cerevisiae proteome reveals the function and cellular localization of the least and most amyloidogenic proteins
Q73912090	Computational analysis of two similar neuropeptides yields distinct conformational ensembles
Q36220263	Computational analysis predicts the Kaposi's sarcoma-associated herpesvirus tegument protein ORF63 to be alpha helical
Q57752565	Computational and experimental approaches for assessing the interactions between the model calycin beta-lactoglobulin and two antibacterial fluoroquinolones
Q85353522	Computational and experimental investigation of constitutive behavior in AraC
Q45193877	Computational and site-specific mutagenesis analyses of the asymmetric charge distribution on calmodulin
Q50469801	Computational approach to site-directed ligand discovery
Q52068726	Computational approach to the protein-folding problem
Q36707980	Computational approaches to study protein unfolding: hen egg white lysozyme as a case study
Q88417979	Computational assessment of folding energy landscapes in heterodimeric coiled coils
Q96767247	Computational backbone design enables soluble engineering of transferrin receptor apical domain
Q33260320	Computational basis of knowledge-based conformational probabilities derived from local- and long-range interactions in proteins.
Q46288028	Computational characterization of substrate and product specificities, and functionality of S-adenosylmethionine binding pocket in histone lysine methyltransferases from Arabidopsis, rice and maize
Q90307930	Computational characterization of the binding mode between oncoprotein Ets-1 and DNA-repair enzymes
Q87015820	Computational characterization of the chemical step in the GTP hydrolysis by Ras-GAP for the wild-type and G13V mutated Ras
Q51322090	Computational characterization of the sequence landscape in simple protein alphabets
Q27643630	Computational design and crystal structure of an enhanced affinity mutant human CD8 alphaalpha coreceptor
Q27647665	Computational design and experimental study of tighter binding peptides to an inactivated mutant of HIV-1 protease
Q54575988	Computational design of a substrate specificity mutant of a protein.
Q35624791	Computational design of protein antigens that interact with the CDR H3 loop of HIV broadly neutralizing antibody 2F5.
Q33991441	Computational design of second-site suppressor mutations at protein-protein interfaces
Q84315163	Computational design, construction, and characterization of a set of specificity determining residues in protein-protein interactions
Q44175684	Computational detection of the binding-site hot spot at the remodeled human growth hormone-receptor interface.
Q30357459	Computational diagnosis of protein conformational diseases: short molecular dynamics simulations reveal a fast unfolding of r-LDL mutants that cause familial hypercholesterolemia.
Q46602224	Computational evidence for the catalytic mechanism of glutaminyl cyclase. A DFT investigation
Q128285726	Computational evidences of a misfolding event in an aggregation‐prone light chain preceding the formation of the non‐native pathogenic dimer
Q38311544	Computational exploration of the activated pathways associated with DNA damage response in breast cancer
Q36065378	Computational exploration of the binding mode of heme-dependent stimulators into the active catalytic domain of soluble guanylate cyclase.
Q41816394	Computational exploration of the network of sequence flow between protein structures
Q51065936	Computational identification of post-translational modification-based nuclear import regulations by characterizing nuclear localization signal-import receptor interaction.
Q33212947	Computational identification of proteins for selectivity assays
Q40288667	Computational identification of self‐inhibitory peptides from envelope proteins
Q46335126	Computational insights into the interaction of the anthrax lethal factor with the N-terminal region of its substrates.
Q51276073	Computational investigation of proton transfer, pKa shifts and pH-optimum of protein-DNA and protein-RNA complexes
Q83742301	Computational investigation of the HIV-1 Rev multimerization using molecular dynamics simulations and binding free energy calculations
Q42694170	Computational methods for identifying a layered allosteric regulatory mechanism for ALS‐causing mutations of Cu‐Zn superoxide dismutase 1
Q31043202	Computational model for the IGF-II/IGF2r complex that is predictive of mutational and surface plasmon resonance data
Q28821078	Computational modeling of laminin N-terminal domains using sparse distance constraints from disulfide bonds and chemical cross-linking
Q26995693	Computational modeling of membrane proteins
Q34668331	Computational modeling of the N-terminus of the human dopamine transporter and its interaction with PIP2 -containing membranes.
Q30353912	Computational mutagenesis studies of protein structure-function correlations.
Q39780607	Computational prediction and analysis of the DR6–NAPP interaction
Q34655493	Computational prediction of the binding site of proteinase 3 to the plasma membrane
Q30157275	Computational protein design as a tool for fold recognition
Q34421580	Computational protein design suggests that human PCNA-partner interactions are not optimized for affinity.
Q52610954	Computational protein design with a generalized Born solvent model: application to Asparaginyl-tRNA synthetase
Q41039615	Computational protein design with explicit consideration of surface hydrophobic patches
Q30157643	Computational protein design with side-chain conformational entropy.
Q48538406	Computational proteomics analysis of HIV-1 protease interactome
Q46486140	Computational proteomics of biomolecular interactions in the sequence and structure space of the tyrosine kinome: deciphering the molecular basis of the kinase inhibitors selectivity
Q57132519	Computational protocol for predicting the binding affinities of zinc containing metalloprotein-ligand complexes
Q40366140	Computational reconstruction of the human skeletal muscle secretome
Q30360277	Computational sidechain placement and protein mutagenesis with implicit solvent models.
Q91226710	Computational simulations of TNF receptor oligomerization on plasma membrane
Q59614315	Computational simulations of stem-cell factor/c-Kit receptor interaction
Q48139800	Computational site-directed mutagenesis studies of the role of the hydrophobic triad on substrate binding in cholesterol oxidase.
Q45125288	Computational studies and peptidomimetic design for the human p53-MDM2 complex
Q46932778	Computational studies of LXR molecular interactions reveal an allosteric communication pathway
Q34372578	Computational studies of colicin insertion into membranes: the closed state
Q70216505	Computational studies of ligand diffusion in globins: I. Leghemoglobin
Q73233208	Computational studies of the domain movement and the catalytic mechanism of thymidine phosphorylase
Q54647155	Computational studies of the interaction between the HIV‐1 integrase tetramer and the cofactor LEDGF/p75: Insights from molecular dynamics simulations and the Informational spectrum method
Q57794928	Computational studies of the structure, dynamics and native content of amyloid-like fibrils of ribonuclease A
Q43797840	Computational study of colipase interaction with lipid droplets and bile salt micelles.
Q61587518	Computational study of lipid-destabilizing protein fragments: Towards a comprehensive view of tilted peptides
Q51628645	Computational study of the Trp-cage miniprotein based on the ECEPP/3 force field
Q43131944	Computational study on the carboligation reaction of acetohidroxyacid synthase: new approach on the role of the HEThDP- intermediate.
Q91802583	Computational study on the selective inhibition mechanism of MS402 to the first and second bromodomains of BRD4
Q27743078	Computational, pulse-radiolytic, and structural investigations of lysine-136 and its role in the electrostatic triad of human C u,Z n superoxide dismutase
Q45039426	Computational, spectroscopic, and resonant mirror biosensor analysis of the interaction of adrenodoxin with native and tryptophan-modified NADPH-adrenodoxin reductase
Q44878988	Computationally accessible method for estimating free energy changes resulting from site-specific mutations of biomolecules: systematic model building and structural/hydropathic analysis of deoxy and oxy hemoglobins
Q30427185	Computationally-predicted CB1 cannabinoid receptor mutants show distinct patterns of salt-bridges that correlate with their level of constitutive activity reflected in G protein coupling levels, thermal stability, and ligand binding
Q30406914	Computed structures of point deletion mutants and their enzymatic activities
Q41749524	Computer analysis of mutations that affect antibody specificity
Q38534207	Computer design of bioactive molecules: a method for receptor-based de novo ligand design
Q46412312	Computer modeling and folding of four-helix bundles
Q74460943	Computer modeling and molecular dynamics simulations of ligand bound complexes of bovine angiogenin: dinucleotide topology at the active site of RNase a family proteins
Q73228386	Computer modeling of human angiogenin-dinucleotide substrate interaction
Q44784434	Computer modeling of the rhamnogalacturonase-"hairy" pectin complex
Q97547599	Computer modelling of a potential agent against SARS-Cov-2 (COVID-19) protease
Q46604460	Computer simulation of antibody binding specificity
Q36251051	Computer simulation study of amyloid fibril formation by palindromic sequences in prion peptides
Q74527953	Computer simulations aimed at structure prediction of supersecondary motifs in proteins
Q73594418	Computer simulations of protein folding by targeted molecular dynamics
Q73393610	Computer simulations of the dynamics of human choriogonadotropin and its alpha subunit
Q73393018	Computer simulations of the properties of the alpha2, alpha2C, and alpha2D de novo designed helical proteins
Q47598356	Computing van der Waals energies in the context of the rotamer approximation.
Q71696573	Configurational effects in antibody-antigen interactions studied by microcalorimetry
Q30327291	Confirmation of a unique intra-dimer cooperativity in the human hemoglobin alpha(1)beta(1)half-oxygenated intermediate supports the symmetry rule model of allosteric regulation.
Q27648764	Conformation and dynamics of the three-helix bundle UBA domain of p62 from experiment and simulation
Q52285629	Conformation and stability of streptokinases from nephritogenic and nonnephritogenic strains of streptococci
Q54129567	Conformation of alamethicin in phospholipid vesicles: implications for insertion models
Q31036408	Conformation of membrane-bound proteins revealed by vacuum-ultraviolet circular-dichroism and linear-dichroism spectroscopy
Q52243196	Conformation of the Ras-binding domain of Raf studied by molecular dynamics and free energy simulations
Q74363297	Conformation of the sebacyl β1Lys82–β2Lys82 crosslink in T-state human hemoglobin
Q46326614	Conformation spaces of proteins
Q42033722	Conformation transition kinetics of Bombyx mori silk protein.
Q46526656	Conformational analysis and design of cross-strand disulfides in antiparallel β-sheets.
Q68151691	Conformational analysis of a 12-residue analogue of mastoparan and of mastoparan X
Q72521328	Conformational analysis of hemopexin by Fourier-transform infrared and circular dichroism spectroscopy
Q36758959	Conformational analysis of protein structures derived from NMR data
Q30371074	Conformational and connotational heterogeneity: a surprising relationship between protein structural flexibility and puns.
Q31141868	Conformational and dynamics changes induced by bile acids binding to chicken liver bile acid binding protein
Q27617580	Conformational and functional variability supported by the BPTI fold: solution structure of the Ca2+ channel blocker calcicludine
Q68596184	Conformational and helicoidal analysis of the molecular dynamics of proteins: "curves," dials and windows for a 50 psec dynamic trajectory of BPTI
Q57829529	Conformational changes in DNA-binding proteins: Relationships with precomplex features and contributions to specificity and stability
Q96292399	Conformational changes in a Vernier zone region: implications for antibody dual specificity
Q44696788	Conformational changes in yeast phosphoglycerate kinase upon ligand binding: fluorescence of a linked probe and chemical reactivity of genetically introduced cysteinyl residues
Q83846383	Conformational changes induced by ATP‐hydrolysis in an ABC transporter: A molecular dynamics study of the Sav1866 exporter
Q68141527	Conformational characteristics of the complete sequence of group A streptococcal M6 protein
Q27644819	Conformational contagion in a protein: structural properties of a chameleon sequence
Q72890874	Conformational deformation in deoxymyoglobin by hydrostatic pressure
Q50042128	Conformational dynamics of L-lysine, L-arginine, L-ornithine binding protein reveals ligand-dependent plasticity
Q40880187	Conformational dynamics of a short antigenic peptide in its free and antibody bound forms gives insight into the role of β-turns in peptide immunogenicity
Q52620670	Conformational dynamics of capping protein and interaction partners: simulation studies
Q73256223	Conformational dynamics of chymotrypsin inhibitor 2 by coarse-grained simulations
Q57875310	Conformational dynamics of cytochrome c: Correlation to hydrogen exchange
Q77977305	Conformational dynamics of cytochrome c: correlation to hydrogen exchange
Q47291196	Conformational dynamics of human protein kinase CK2α and its effect on function and inhibition.
Q30370239	Conformational dynamics of nonsynonymous variants at protein interfaces reveals disease association.
Q42012774	Conformational dynamics of recoverin's Ca2+‐myristoyl switch probed by 15N NMR relaxation dispersion and chemical shift analysis
Q54770451	Conformational dynamics of the EGFR kinase domain reveals structural features involved in activation.
Q33743239	Conformational flexibility and binding interactions of the G protein βγ heterodimer
Q27648040	Conformational flexibility in mammalian 15S-lipoxygenase: Reinterpretation of the crystallographic data
Q82627881	Conformational flexibility may explain multiple cellular roles of PEST motifs
Q54457701	Conformational flexibility of RecA protein filament: transitions between compressed and stretched states
Q52450208	Conformational flexibility of a scorpion toxin active on mammals and insects: a circular dichroism study
Q73594370	Conformational flexibility of the catalytic Asp dyad in HIV-1 protease: An ab initio study on the free enzyme
Q48294286	Conformational flexibility of the complete catalytic domain of Cdc25B phosphatases
Q30380926	Conformational fluctuations of the AXH monomer of Ataxin-1.
Q46595057	Conformational interconversion in compstatin probed with molecular dynamics simulations
Q44253632	Conformational mapping of a viral fusion peptide in structure-promoting solvents using circular dichroism and electrospray mass spectrometry
Q41860440	Conformational perturbation of interleukin-2: a strategy for the design of cytokine analogs
Q43986867	Conformational polymorphism of wild-type and mutant prion proteins: Energy landscape analysis
Q33399171	Conformational preferences of a short Aib/Ala-based water-soluble peptide as a function of temperature
Q54644212	Conformational regulation of the EGFR kinase core by the juxtamembrane and C‐terminal tail: A molecular dynamics study
Q30163865	Conformational sampling and dynamics of membrane proteins from 10-nanosecond computer simulations.
Q91327312	Conformational sampling and polarization of Asp26 in pKa calculations of thioredoxin
Q30424944	Conformational sampling by NMR solution structures calculated with the program DIANA evaluated by comparison with long-time molecular dynamics calculations in explicit water
Q43280889	Conformational selection and collagenolysis in type III collagen
Q54335575	Conformational selection and induced changes along the catalytic cycle of Escherichia coli dihydrofolate reductase.
Q45965729	Conformational selection in silico: loop latching motions and ligand binding in enzymes.
Q57077666	Conformational selection through electrostatics: Free energy simulations of gtp and gdp binding to archaeal initiation factor 2
Q28569677	Conformational stability and DNA binding energetics of the rat thyroid transcription factor 1 homeodomain
Q100318080	Conformational stability of the bacterial adhesin, FimH, with an inactivating mutation
Q48117891	Conformational stability of the epidermal growth factor (EGF) receptor as influenced by glycosylation, dimerization and EGF hormone binding.
Q79909276	Conformational states and folding pathways of peptides revealed by principal-independent component analyses
Q30331653	Conformational states of the glucocorticoid receptor DNA-binding domain from molecular dynamics simulations.
Q48007456	Conformational subspace in simulation of early-stage protein folding
Q27694586	Conformational transitions driven by pyridoxal-5'-phosphate uptake in the psychrophilic serine hydroxymethyltransferase from Psychromonas ingrahamii
Q47958933	Conformational variability of the stationary phase survival protein E from Xylella fastidiosa revealed by X-ray crystallography, small-angle X-ray scattering studies, and normal mode analysis.
Q27621091	Conformational variation of calcium-bound troponin C
Q50791664	Conformations of variably linked chimeric proteins evaluated by synchrotron X-ray small-angle scattering.
Q40966790	Confronting the problem of interconnected structural changes in the comparative modeling of proteins.
Q47318855	Congruent qualitative behavior of complete and reconstructed phase space trajectories from biomolecular dynamics simulation
Q32105094	ConsDock: A new program for the consensus analysis of protein-ligand interactions
Q36788610	Consensus preferred hydration sites in six FKBP12-drug complexes.
Q24657210	Consensus scoring for enriching near-native structures from protein-protein docking decoys
Q86493482	Conservation analysis of class-specific positions in cytochrome P450 monooxygenases: functional and structural relevance
Q44379456	Conservation and amyloid formation: a study of the gelsolin-like family
Q30419557	Conservation and prediction of solvent accessibility in protein families
Q30349854	Conservation of cis prolyl bonds in proteins during evolution.
Q80060137	Conservation of metal-coordinating residues
Q47621019	Conservation of polar residues as hot spots at protein interfaces
Q57808046	Conservation of polar residues as hot spots at protein interfaces
Q54204143	Conservation of structural fluctuations in homologous protein kinases and its implications on functional sites
Q44236368	Conserved amino acid networks involved in antibody variable domain interactions
Q84248139	Conserved conformational dynamics of membrane fusion protein transmembrane domains and flanking regions indicated by sequence statistics
Q30779887	Conserved core structure and active site residues in alkaline phosphatase superfamily enzymes
Q97533172	Conserved internal hydration motifs in protein kinases
Q30327615	Conserved key amino acid positions (CKAAPs) derived from the analysis of common substructures in proteins.
Q41969439	Conserved movement of TMS11 between occluded conformations of LacY and XylE of the major facilitator superfamily suggests a similar hinge-like mechanism
Q27640839	Conserved protein YecM fromEscherichia coli shows structural homology to metal-binding isomerases and oxygenases
Q27330867	Conserved quantitative stability/flexibility relationships (QSFR) in an orthologous RNase H pair
Q30333118	Conserved residue clustering and protein structure prediction.
Q30909739	Conserved spatially interacting motifs of protein superfamilies: application to fold recognition and function annotation of genome data
Q83248552	Conserved structural and dynamics features in the denatured states of drosophila SUMO, human SUMO and ubiquitin proteins: Implications to sequence-folding paradigm
Q27642612	Conserved structural elements in glutathione transferase homologues encoded in the genome of Escherichia coli
Q27618712	Conserved water molecules in a large family of microbial ribonucleases
Q74093196	Conserved water molecules in the specificity pocket of serine proteases and the molecular mechanism of Na+ binding
Q99553570	Consistency and variation of protein subcellular location annotations
Q30332520	Consistency matrices: quantified structure alignments for sets of related proteins.
Q28286468	Consistent refinement of submitted models at CASP using a knowledge-based potential
Q35382958	Constant pH molecular dynamics of proteins in explicit solvent with proton tautomerism
Q62764040	Constant-pH molecular dynamics using continuous titration coordinates
Q46586536	Constitutive and dynamic phosphorylation and acetylation sites on NUCKS, a hypermodified nuclear protein, studied by quantitative proteomics
Q30375694	Construct optimization for protein NMR structure analysis using amide hydrogen/deuterium exchange mass spectrometry.
Q30424569	Constructing amino acid residue substitution classes maximally indicative of local protein structure
Q51914305	Constructing ensembles of flexible fragments in native proteins by iterative stochastic elimination is relevant to protein-protein interfaces
Q30369013	Constructing templates for protein structure prediction by simulation of protein folding pathways.
Q73083592	Construction and analysis of a detailed three-dimensional model of the ligand binding domain of the human B cell receptor CD40
Q78315721	Construction and characterization of beta-lactoglobulin chimeras
Q52007588	Construction of molecular assemblies via docking: modeling of tetramers with D2 symmetry
Q51838200	Contact order dependent protein folding rates: kinetic consequences of a cooperative interplay between favorable nonlocal interactions and local conformational preferences.
Q51088346	Contact patterns between helices and strands of sheet define protein folding patterns
Q30386605	Contact prediction for beta and alpha-beta proteins using integer linear optimization and its impact on the first principles 3D structure prediction method ASTRO-FOLD.
Q44547214	Contact prediction using mutual information and neural nets
Q41003317	Contact rearrangements form coupled networks from local motions in allosteric proteins
Q30382587	Contact-assisted protein structure modeling by global optimization in CASP11.
Q39015550	Context characterization of amino acid homorepeats using evolution, position, and order
Q51906237	Context shapes: Efficient complementary shape matching for protein-protein docking.
Q34713866	Context-specific amino acid substitution matrices and their use in the detection of protein homologs
Q47361657	Continuous Automated Model EvaluatiOn (CAMEO) complementing the critical assessment of structure prediction in CASP12.
Q68697928	Continuous compact protein domains
Q43825577	Continuum electrostatic analysis of irregular ionization and proton allocation in proteins
Q33179640	Continuum electrostatic analysis of preferred solvation sites around proteins in solution
Q58489183	Continuum electrostatic analysis of preferred solvation sites around proteins in solution
Q52421623	Continuum electrostatics of the C-peptide: anatomy of the problem
Q27634694	Contribution of Thr29 to the thermodynamic stability of goat alpha-lactalbumin as determined by experimental and theoretical approaches
Q53988252	Contribution of arginine (HC3) 141 alpha to the Bohr effect of the fourth binding step in the reaction of ligand with human hemoglobin
Q46377411	Contributions of water transfer energy to protein-ligand association and dissociation barriers: Watermap analysis of a series of p38α MAP kinase inhibitors
Q43947466	Contributions to the binding free energy of ligands to avidin and streptavidin.
Q38288280	Control of crystal forms of apoferritin by site-directed mutagenesis
Q51000031	Conventional NMA as a better standard for evaluating elastic network models
Q79624906	Convergence of molecular dynamics simulations of membrane proteins
Q42807058	Conversion of type I 4:6 to 3:5 beta-turn types in human acidic fibroblast growth factor: effects upon structure, stability, folding, and mitogenic function.
Q46402210	Conversion of yeast phosphoglycerate kinase into amyloid-like structure
Q30323184	Cooperative approach for the protein fold recognition.
Q31913202	Cooperative binding of inhaled anesthetics and ATP to firefly luciferase
Q31001659	Cooperative effects in hydrogen-bonding of protein secondary structure elements: a systematic analysis of crystal data using Secbase.
Q73271590	Cooperative fluctuations of unliganded and substrate-bound HIV-1 protease: a structure-based analysis on a variety of conformations from crystallography and molecular dynamics simulations
Q57905970	Cooperative folding mechanism of a β-hairpin peptide studied by a multicanonical replica-exchange molecular dynamics simulation
Q43028867	Cooperative helix stabilization by complex Arg-Glu salt bridges.
Q42182110	Cooperative nature of gating transitions in K(+) channels as seen from dynamic importance sampling calculations
Q27643950	Cooperative propagation of local stability changes from low-stability and high-stability regions in a SH3 domain
Q80809761	Cooperative symmetric to asymmetric conformational transition of the apo-form of scavenger decapping enzyme revealed by simulations
Q74460955	Coordination topology and stability for the native and binding conformers of chymotrypsin inhibitor 2
Q50085600	Copper binding sites in the C-terminal domain of mouse prion protein: A hybrid (QM/MM) molecular dynamics study
Q86534359	Copper-chaperones with dicoordinated Cu(I)--unique protection mechanism
Q93555607	Correction
Q125757087	Correction to the article “Crystal Structure of a Ferredoxin Reductase for the CYP199A2 System from Rhodopseudomonas palustris ”
Q57082065	Correction to the article “Position-resolved free energy of solvation for amino acids in lipid membranes from molecular dynamics simulations”
Q46093741	Correlated mutation analyses on super-family alignments reveal functionally important residues
Q25891592	Correlated mutations and residue contacts in proteins
Q80701899	Correlated mutations at gp120 positions 322 and 440: implications for gp120 structure
Q47603699	Correlated mutations: advances and limitations. A study on fusion proteins and on the Cohesin-Dockerin families
Q52082395	Correlation between changes in nuclear magnetic resonance order parameters and conformational entropy: molecular dynamics simulations of native and denatured staphylococcal nuclease
Q41675264	Correlation between knowledge-based and detailed atomic potentials: application to the unfolding of the GCN4 leucine zipper
Q72834590	Correlation between protein stability and crystal properties of designed ROP variants
Q30385358	Correlation of (2)J couplings with protein secondary structure.
Q57980270	Correlation of the enzyme activities of Bacillus stearothermophilus lactate dehydrogenase on three substrates with the results of molecular dynamics/energy minimization conformational searching
Q73784287	Correlation of the enzyme activities of Bacillus stearothermophilus lactate dehydrogenase on three substrates with the results of molecular dynamics/energy minimization conformational searching
Q45211190	Correlations of atomic movements in lysozyme crystals
Q31014050	Correspondence of function and phylogeny of ABC proteins based on an automated analysis of 20 model protein data sets.
Q51520168	Coupling between ATP hydrolysis and protein conformational change in maltose transporter
Q51967605	Coupling between conformation and proton binding in proteins
Q30374017	Coupling between overall rotational diffusion and domain motions in proteins and its effect on dielectric spectra.
Q92372186	Coupling dynamics and evolutionary information with structure to identify protein regulatory and functional binding sites
Q43956362	Coupling of ligand binding and dimerization of helix-loop-helix peptides: spectroscopic and sedimentation analyses of calbindin D9k EF-hands
Q60459586	Coupling of structural fluctuations to deamidation reaction in triosephosphate isomerase by Gaussian network model
Q46470076	Coupling of the guanosine glycosidic bond conformation and the ribonucleotide cleavage reaction: implications for barnase catalysis
Q52072063	Covariance analysis of protein families: the case of the variable domains of antibodies
Q123218872	Cover Image, Volume 84, Issue 10
Q63247875	Cover Image, Volume 85, Issue 2
Q58482678	Cover Image, Volume 85, Issue 3
Q128879200	Cover Image, Volume 86, Issue 11
Q57276435	Cover Image, Volume 86, Issue 5
Q128050175	Cover Image, Volume 87, Issue 6
Q127758967	Cover Image, Volume 87, Issue 7
Q128271530	Cover Image, Volume 88, Issue 8
Q84312224	Cover and spacer insertions: small nonhydrophobic accessories that assist protein oligomerization
Q51145762	Criteria for downhill protein folding: calorimetry, chevron plot, kinetic relaxation, and single-molecule radius of gyration in chain models with subdued degrees of cooperativity
Q30429619	Criteria for evaluating protein structures derived from comparative modeling
Q67961445	Criteria that discriminate between native proteins and incorrectly folded models
Q39540848	Critical analysis of the successes and failures of homology models of G protein-coupled receptors.
Q30351462	Critical assessment of methods of protein structure prediction (CASP)--round 6.
Q29048192	Critical assessment of methods of protein structure prediction (CASP)--round IX
Q29048203	Critical assessment of methods of protein structure prediction (CASP)--round x
Q46348067	Critical assessment of methods of protein structure prediction (CASP)-Round XII.
Q90564393	Critical assessment of methods of protein structure prediction (CASP)-Round XIII
Q30336229	Critical assessment of methods of protein structure prediction (CASP)-round V.
Q56171911	Critical assessment of methods of protein structure prediction (CASP): Round II
Q30429616	Critical assessment of methods of protein structure prediction (CASP): round II.
Q30323113	Critical assessment of methods of protein structure prediction (CASP): round III.
Q30329564	Critical assessment of methods of protein structure prediction (CASP): round IV.
Q47588454	Critical assessment of methods of protein structure prediction - Round VIII.
Q24642528	Critical assessment of methods of protein structure prediction-Round VII
Q30388020	Critical assessment of methods of protein structure prediction: Progress and new directions in round XI.
Q51932994	Critical assessment of the automated AutoDock as a new docking tool for virtual screening
Q51930103	Critical evaluation of methods to incorporate entropy loss upon binding in high-throughput docking
Q74252623	Critical evaluation of the research docking program for the CASP2 challenge
Q130038794	Critical micellar concentration determination of pure phospholipids and lipid‐raft and their mixtures with cholesterol
Q50936574	Cross-talk between the ligand- and DNA-binding domains of estrogen receptor
Q79554814	Crosstalk between the subunits of the homodimeric enzyme triosephosphate isomerase
Q48044614	Cry1A(b)16 toxin from Bacillus thuringiensis: Theoretical refinement of three-dimensional structure and prediction of peptides as molecular markers for detection of genetically modified organisms
Q90430303	Cryo-electron microscopy targets in CASP13: Overview and evaluation of results
Q43629663	Cryptic epitopes in N-terminally truncated prion protein are exposed in the full-length molecule: dependence of conformation on pH.
Q90653368	Crystal and solution structures of human oncoprotein Musashi-2 N-terminal RNA recognition motif 1
Q51975331	Crystal packing effects on protein loops
Q27635348	Crystal packing interaction that blocks crystallization of a site-specific DNA binding protein-DNA complex
Q27670601	Crystal packing modifies ligand binding affinity: The case of aldose reductase
Q67777637	Crystal parameters and molecular replacement of an anticholera toxin peptide complex
Q27646971	Crystal structure analysis reveals a novel forkhead-associated domain of ESAT-6 secretion system C protein in Staphylococcus aureus
Q48043033	Crystal structure analysis, covalent docking, and molecular dynamics calculations reveal a conformational switch in PhaZ7 PHB depolymerase
Q36479423	Crystal structure and biochemical properties of putrescine carbamoyltransferase from Enterococcus faecalis: Assembly, active site, and allosteric regulation
Q27649935	Crystal structure and domain characterization of ScpB from Mycobacterium tuberculosis
Q27656246	Crystal structure and enhanced activity of a cutinase-like enzyme from Cryptococcus sp. strain S-2
Q27676871	Crystal structure and fluorescence studies reveal the role of helical dimeric interface of staphylococcal FabG1 in positive cooperativity for NADPH
Q27649048	Crystal structure and functional analysis identify the P-loop containing protein YFH7 of Saccharomyces cerevisiae as an ATP-dependent kinase
Q27682287	Crystal structure and nucleic acid‐binding activity of the CRISPR‐associated protein Csx1 of Pyrococcus furiosus
Q27659268	Crystal structure and oligomeric state of the RetS signaling kinase sensory domain
Q27649852	Crystal structure and possible dimerization of the single RRM of human PABPN1
Q27647394	Crystal structure and putative function of small Toprim domain-containing protein from Bacillus stearothermophilus
Q27627763	Crystal structure and refolding properties of the mutant F99S/M153T/V163A of the green fluorescent protein
Q27649511	Crystal structure and stereochemical studies of KD(P)G aldolase from Thermoproteus tenax
Q46634395	Crystal structure and structural stability of acylphosphatase from hyperthermophilic archaeon Pyrococcus horikoshii OT3.
Q27666584	Crystal structure and substrate-binding mode of cellulase 12A from Thermotoga maritima
Q27654048	Crystal structure and thermodynamic analysis of diagnostic mAb 106.3 complexed with BNP 5-13 (C10A)
Q46900611	Crystal structure at 1.45-A resolution of the major allergen endo-beta-1,3-glucanase of banana as a molecular basis for the latex-fruit syndrome
Q27688953	Crystal structure determination of anti-DNA Fab A52
Q27649051	Crystal structure of 2-keto-3-deoxygluconate kinase (TM0067) from Thermotoga maritima at 2.05 A resolution
Q34559842	Crystal structure of 2-phosphosulfolactate phosphatase (ComB) from Clostridium acetobutylicum at 2.6 A resolution reveals a new fold with a novel active site
Q27664979	Crystal structure of 3-hexulose-6-phosphate synthase, a member of the orotidine 5'-monophosphate decarboxylase suprafamily
Q53590741	Crystal structure of 5'-methylthioadenosine nucleosidase from Arabidopsis thaliana at 1.5-A resolution
Q27683480	Crystal structure of 6-guanidinohexanoyl trypsin near the optimum pH reveals the acyl-enzyme intermediate to be deacylated
Q40733218	Crystal structure of A. aeolicus LpxC with bound product suggests alternate deacetylation mechanism
Q27645431	Crystal structure of ACE19, the collagen binding subdomain of Enterococus faecalis surface protein ACE
Q46815510	Crystal structure of ADP/AMP complex of Escherichia coli adenylate kinase
Q27649816	Crystal structure of AICAR transformylase IMP cyclohydrolase (TM1249) from Thermotoga maritima at 1.88 A resolution
Q89857932	Crystal structure of Alr1298, a pentapeptide repeat protein from the cyanobacterium Nostoc sp. PCC 7120, determined at 2.1 Å resolution
Q27673831	Crystal structure of Arabidopsis thaliana 12‐oxophytodienoate reductase isoform 3 in complex with 8‐iso prostaglandin A1
Q27648398	Crystal structure of Arabidopsis thaliana cytokinin dehydrogenase
Q27656983	Crystal structure of Arabidopsis translation initiation factor eIF-5A2
Q63351983	Crystal structure of At2g03760, a putative steroid sulfotransferase from Arabidopsis thaliana
Q52371520	Crystal structure of B-cell co-receptor CD19 in complex with antibody B43 reveals an unexpected fold
Q27650586	Crystal structure of B. subtilis YjcG characterizing the YjcG-like group of 2H phosphoesterase superfamily
Q27648945	Crystal structure of Bacillus subtilis CodW, a noncanonical HslV-like peptidase with an impaired catalytic apparatus
Q37471276	Crystal structure of Bacillus subtilis YdaF protein: a putative ribosomal N-acetyltransferase.
Q27639347	Crystal structure of Bacillus subtilis ioli shows endonuclase IV fold with altered Zn binding
Q27667879	Crystal structure of Bacteroides thetaiotaomicron TetX2: A tetracycline degrading monooxygenase at 2.8 Å resolution
Q27690806	Crystal structure of BinB: a receptor binding component of the binary toxin from Lysinibacillus sphaericus
Q27621079	Crystal structure of CHO reductase, a member of the aldo-keto reductase superfamily
Q27732095	Crystal structure of CTP-ligated T state aspartate transcarbamoylase at 2.5 A resolution: implications for ATCase mutants and the mechanism of negative cooperativity
Q47683950	Crystal structure of D-glycero-Β-D-manno-heptose-1-phosphate adenylyltransferase from Burkholderia pseudomallei
Q27639588	Crystal structure of D-ribose-5-phosphate isomerase (RpiA) from Escherichia coli
Q27650422	Crystal structure of DFA0005 complexed with alpha-ketoglutarate: a novel member of the ICL/PEPM superfamily from alkali-tolerant Deinococcus ficus
Q27678498	Crystal structure of DeSI-1, a novel deSUMOylase belonging to a putative isopeptidase superfamily
Q27646879	Crystal structure of Dim2p: a preribosomal RNA processing factor, from Pyrococcus horikoshii OT3 at 2.30 A
Q27689019	Crystal structure of DszC from Rhodococcus sp. XP at 1.79 Å
Q44855362	Crystal structure of E. coli yddE protein reveals a striking homology with diaminopimelate epimerase
Q46801612	Crystal structure of Escherichia coli DkgA, a broad-specificity aldo-keto reductase
Q27730949	Crystal structure of Escherichia coli RNase HI in complex with Mg2+ at 2.8 A resolution: proof for a single Mg(2+)-binding site
Q27731984	Crystal structure of Escherichia coli TEM1 beta-lactamase at 1.8 A resolution
Q46529634	Crystal structure of Escherichia coli YfhJ protein, a member of the ISC machinery involved in assembly of iron-sulfur clusters
Q27617728	Crystal structure of Escherichia coli uracil DNA glycosylase and its complexes with uracil and glycerol: structure and glycosylase mechanism revisited
Q27670731	Crystal structure of FAF1 UBX domain in complex with p97/VCP N domain reveals a conformational change in the conserved FcisP touch‐turn motif of UBX domain
Q27650274	Crystal structure of GH13 alpha-glucosidase GSJ from one of the deepest sea bacteria
Q28256757	Crystal structure of GlcAT-S, a human glucuronyltransferase, involved in the biosynthesis of the HNK-1 carbohydrate epitope
Q54623889	Crystal structure of HP0242, a hypothetical protein from Helicobacter pylori with a novel fold.
Q27666850	Crystal structure of HP0721, a novel secreted protein from Helicobacter pylori
Q27644051	Crystal structure of Helicobacter pylori spermidine synthase: a Rossmann-like fold with a distinct active site
Q24297467	Crystal structure of Homo sapiens protein LOC79017
Q57973457	Crystal structure of Homo sapiens protein hp14.5
Q34302791	Crystal structure of Homo sapiens protein hp14.5.
Q34510806	Crystal structure of Homo sapiens thialysine Nepsilon-acetyltransferase (HsSSAT2) in complex with acetyl coenzyme A.
Q56978825	Crystal structure of Hsp33 chaperone (TM1394) from Thermotoga maritima at 2.20 Å resolution
Q27689666	Crystal structure of JHP933 from Helicobacter pylori J99 shows two-domain architecture with a DUF1814 family nucleotidyltransferase domain and a helical bundle domain
Q27654047	Crystal structure of KaiC-like protein PH0186 from hyperthermophilic archaea Pyrococcus horikoshii OT3
Q27653395	Crystal structure of LZ-8 from the medicinal fungus Ganoderma lucidium
Q27639581	Crystal structure of MTH169, a crucial component of phosphoribosylformylglycinamidine synthetase
Q27638994	Crystal structure of Methanobacterium thermoautotrophicum conserved protein MTH1020 reveals an NTN-hydrolase fold
Q27646884	Crystal structure of MtnX phosphatase from Bacillus subtilis at 2.0 angstroms resolution provides a structural basis for bipartite phosphomonoester hydrolysis of 2-hydroxy-3-keto-5-methylthiopentenyl-1-phosphate
Q27687101	Crystal structure of Mycobacterium tuberculosis CarD, an essential RNA polymerase binding protein, reveals a quasidomain-swapped dimeric structural architecture
Q27658106	Crystal structure of Mycobacterium tuberculosis LppA, a lipoprotein confined to pathogenic mycobacteria
Q27673650	Crystal structure of Mycobacterium tuberculosis Rv3168: A putative aminoglycoside antibiotics resistance enzyme
Q27649623	Crystal structure of N-acylamino acid racemase from Thermus thermophilus HB8
Q27658679	Crystal structure of NADH:rubredoxin oxidoreductase from Clostridium acetobutylicum: a key component of the dioxygen scavenging system in obligatory anaerobes
Q45220727	Crystal structure of NH3-dependent NAD+ synthetase from Helicobacter pylori.
Q27646784	Crystal structure of NMA1982 from Neisseria meningitidis at 1.5 angstroms resolution provides a structural scaffold for nonclassical, eukaryotic-like phosphatases
Q27649774	Crystal structure of Natratoxin, a novel snake secreted phospholipaseA2 neurotoxin from Naja atra venom inhibiting A-type K+ currents
Q27682234	Crystal structure of NirD, the small subunit of the nitrite reductase NirbD from Mycobacterium tuberculosis at 2.0 Å resolution
Q27653171	Crystal structure of Npun_R1517, a putative negative regulator of heterocyst differentiation from Nostoc punctiforme PCC 73102
Q27655646	Crystal structure of NusG N-terminal (NGN) domain from Methanocaldococcus jannaschii and its interaction with rpoE''
Q46475143	Crystal structure of O-acetylserine sulfhydrylase (TM0665) from Thermotoga maritima at 1.8 A resolution
Q27650276	Crystal structure of PAE0151 from Pyrobaculum aerophilum, a PIN-domain (VapC) protein from a toxin-antitoxin operon
Q34370302	Crystal structure of PH0010 from Pyrococcus horikoshii, which is highly homologous to human AMMECR 1C-terminal region.
Q27652349	Crystal structure of PH1733, an aspartate racemase homologue, from Pyrococcus horikoshii OT3
Q27658491	Crystal structure of PRY-SPRY domain of human TRIM72
Q102382264	Crystal structure of PYCH_01220 from Pyrococcus yayanosii potentially involved in binding nucleic acid
Q27687798	Crystal structure of Plasmodium vivax FK506-binding protein 25 reveals conformational changes responsible for its noncanonical activity
Q28268145	Crystal structure of PqqC from Klebsiella pneumoniae at 2.1 A resolution
Q46683357	Crystal structure of PurE (BA0288) from Bacillus anthracis at 1.8 A resolution
Q27643807	Crystal structure of Pyrococcus horikoshii PPC protein at 1.60 A resolution
Q27650644	Crystal structure of QueC from Bacillus subtilis: an enzyme involved in preQ1 biosynthesis
Q27652872	Crystal structure of RecX: a potent regulatory protein of RecA from Xanthomonas campestris
Q34410412	Crystal structure of S-adenosylmethionine:tRNA ribosyltransferase-isomerase (QueA) from Thermotoga maritima at 2.0 A resolution reveals a new fold
Q27644647	Crystal structure of S. aureus YlaN, an essential leucine rich protein involved in the control of cell shape
Q27649936	Crystal structure of STS042, a stand-alone RAM module protein, from hyperthermophilic archaeon Sulfolobus tokodaii strain 7
Q27654994	Crystal structure of Saccharomyces cerevisiae Ygr203w, a homolog of single-domain rhodanese and Cdc25 phosphatase catalytic domain
Q27654407	Crystal structure of Saccharomyces cerevisiae glutamine synthetase Gln1 suggests a nanotube-like supramolecular assembly
Q46203974	Crystal structure of ScpB from Chlorobium tepidum, a protein involved in chromosome partitioning
Q27677025	Crystal structure of SsfS6, the putativeC-glycosyltransferase involved in SF2575 biosynthesis
Q27667654	Crystal structure of Sulfolobus tokodaii Sua5 complexed with L-threonine and AMPPNP
Q72668315	Crystal structure of TGF-beta 2 refined at 1.8 A resolution
Q27644506	Crystal structure of TM1030 from Thermotoga maritima at 2.3 A resolution reveals molecular details of its transcription repressor function
Q46245319	Crystal structure of TM1367 from Thermotoga maritima at 1.90 A resolution reveals an atypical member of the cyclophilin (peptidylprolyl isomerase) fold
Q57894979	Crystal structure of TT1662 from Thermus thermophilus HB8: A member of the α/β hydrolase fold enzymes
Q27649050	Crystal structure of TTHA0303 (TT2238), a four-helix bundle protein with an exposed histidine triad from Thermus thermophilus HB8 at 2.0 A
Q27657213	Crystal structure of TTHA0807, a CcpA regulator, from Thermus thermophilus HB8
Q27653940	Crystal structure of TTHA1264, a putative M16-family zinc peptidase from Thermus thermophilus HB8 that is homologous to the beta subunit of mitochondrial processing peptidase
Q27651934	Crystal structure of TTHA1429, a novel metallo-beta-lactamase superfamily protein from Thermus thermophilus HB8
Q27643234	Crystal structure of TTHA1657 (AT-rich DNA-binding protein; p25) from Thermus thermophilus HB8 at 2.16 A resolution
Q27650417	Crystal structure of Tflp: a ferredoxin-like metallo-beta-lactamase superfamily protein from Thermoanaerobacter tengcongensis
Q27652348	Crystal structure of Thermotoga maritima SPOUT superfamily RNA methyltransferase Tm1570 in complex with S-adenosyl-L-methionine
Q27666636	Crystal structure of Toll-like receptor 2-activating lipoprotein IIpA from Vibrio vulnificus
Q53584302	Crystal structure of UDP-N-acetylenolpyruvylglucosamine reductase (MurB) from Thermus caldophilus
Q27649770	Crystal structure of UDP-N-acetylglucosamine enolpyruvyl transferase from Haemophilus influenzae in complex with UDP-N-acetylglucosamine and fosfomycin
Q27642422	Crystal structure of UDP‐N‐acetylglucosamine acyltransferase fromHelicobacter pylori
Q82649965	Crystal structure of VC0702 at 2.0 A: conserved hypothetical protein from Vibrio cholerae
Q27649938	Crystal structure of VC1805, a conserved hypothetical protein from a Vibrio cholerae pathogenicity island, reveals homology to human p32
Q79212146	Crystal structure of XC5357 from Xanthomonas campestris: a putative tetracenomycin polyketide synthesis protein adopting a novel cupin subfamily structure
Q46602324	Crystal structure of YHI9, the yeast member of the phenazine biosynthesis PhzF enzyme superfamily
Q47714904	Crystal structure of YIGZ, a conserved hypothetical protein from Escherichia coli k12 with a novel fold
Q27650143	Crystal structure of YagE, a putative DHDPS-like protein from Escherichia coli K12
Q27640186	Crystal structure of YbaB from Haemophilus influenzae (HI0442), a protein of unknown function coexpressed with the recombinational DNA repair protein RecR
Q27622559	Crystal structure of YbaK protein from Haemophilus influenzae (HI1434) at 1.8 A resolution: functional implications
Q27642257	Crystal structure of YdcE protein from Bacillus subtilis
Q27636863	Crystal structure of Yeco from Haemophilus influenzae (HI0319) reveals a methyltransferase fold and a bound S‐adenosylhomocysteine
Q79969417	Crystal structure of YfiR, an unusual TetR/CamR-type putative transcriptional regulator from Bacillus subtilis
Q27650764	Crystal structure of YlqF, a circularly permuted GTPase: implications for its GTPase activation in 50 S ribosomal subunit assembly
Q27697926	Crystal structure of YwpF from Staphylococcus aureus reveals its architecture comprised of a β-barrel core domain resembling type VI secretion system proteins and a two-helix pair
Q27652876	Crystal structure of a 1.6-hexanediol bound tetrameric form of Escherichia coli lac-repressor refined to 2.1 A resolution
Q98161415	Crystal structure of a 123 amino acids dimerization domain of Drosophila Caprin
Q27648489	Crystal structure of a 3-oxoacyl-(acylcarrier protein) reductase (BA3989) from Bacillus anthracis at 2.4-A resolution
Q27678203	Crystal structure of a Cas6 paralogous protein from Pyrococcus furiosus
Q27690169	Crystal structure of a Chlamydomonas reinhardtii flagellar RabGAP TBC-domain at 1.8 Å resolution
Q46294475	Crystal structure of a PIN (PilT N-terminus) domain (AF0591) from Archaeoglobus fulgidus at 1.90 A resolution
Q27650583	Crystal structure of a PduO-type ATP:cobalamin adenosyltransferase from Burkholderia thailandensis
Q98896987	Crystal structure of a SAM-dependent O-methyltransferase-like enzyme from Aspergillus flavus
Q27704892	Crystal structure of a [NiFe] hydrogenase maturation protease HybD from Thermococcus kodakarensis KOD1
Q27666625	Crystal structure of a bacterial phosphoglucomutase, an enzyme involved in the virulence of multiple human pathogens
Q46389037	Crystal structure of a bicupin protein HutD involved in histidine utilization in Pseudomonas.
Q27644364	Crystal structure of a binary complex between human GCN5 histone acetyltransferase domain and acetyl coenzyme A
Q38328070	Crystal structure of a calcium-induced dimer of two isoforms of cobra phospholipase A2 at 1.6 A resolution
Q27650765	Crystal structure of a chimera of human and Plasmodium falciparum hypoxanthine guanine phosphoribosyltransferases provides insights into oligomerization
Q27765347	Crystal structure of a complex formed between proteolytically-generated lactoferrin fragment and proteinase K
Q45194395	Crystal structure of a component of glycine cleavage system: T-protein from Pyrococcus horikoshii OT3 at 1.5 A resolution.
Q57839935	Crystal structure of a consensus-designed ankyrin repeat protein: Implications for stability
Q56978807	Crystal structure of a conserved hypothetical protein (gi: 13879369) from Mouse at 1.90 Å resolution reveals a new fold
Q57895178	Crystal structure of a conserved hypothetical protein TT1751 fromThermus thermophilus HB8
Q27648693	Crystal structure of a conserved protein of unknown function (MJ1651) from Methanococcus jannaschii
Q27644821	Crystal structure of a cyanobacterial sucrose-phosphatase in complex with glucose-containing disaccharides
Q27651674	Crystal structure of a family GT4 glycosyltransferase from Bacillus anthracis ORF BA1558
Q27656658	Crystal structure of a ferredoxin reductase for the CYP199A2 system from Rhodopseudomonas palustris
Q57898162	Crystal structure of a feruloyl esterase belonging to the tannase family: A disulfide bond near a catalytic triad
Q27641821	Crystal structure of a flavin-binding protein from Thermotoga maritima
Q34384467	Crystal structure of a formiminotetrahydrofolate cyclodeaminase (TM1560) from Thermotoga maritima at 2.80 A resolution reveals a new fold
Q35536516	Crystal structure of a fully glycosylated HIV-1 gp120 core reveals a stabilizing role for the glycan at Asn262.
Q56978662	Crystal structure of a glycerate kinase (TM1585) from Thermotoga maritima at 2.70 Å resolution reveals a new fold
Q46714134	Crystal structure of a glycerophosphodiester phosphodiesterase (GDPD) from Thermotoga maritima (TM1621) at 1.60 A resolution
Q46803204	Crystal structure of a heterodimer of phospholipase A2 from Naja naja sagittifera at 2.3 A resolution reveals the presence of a new PLA2-like protein with a novel cys 32-Cys 49 disulphide bridge with a bound sugar at the substrate-binding site
Q27643947	Crystal structure of a histidine kinase sensor domain with similarity to periplasmic binding proteins
Q34447851	Crystal structure of a human kynurenine aminotransferase II homologue from Pyrococcus horikoshii OT3 at 2.20 A resolution.
Q27640465	Crystal structure of a hypothetical protein, TM841 of Thermotoga maritima, reveals its function as a fatty acid-binding protein
Q27642420	Crystal structure of a hypothetical protein, TT1725, from Thermus thermophilus HB8 at 1.7 A resolution
Q27679089	Crystal structure of a member of a novel family of dioxygenases (PF10014) reveals a conserved cupin fold and active site
Q27667656	Crystal structure of a metal-dependent phosphoesterase (YP_910028.1) from Bifidobacterium adolescentis: Computational prediction and experimental validation of phosphoesterase activity
Q44947551	Crystal structure of a methionine aminopeptidase (TM1478) from Thermotoga maritima at 1.9 A resolution
Q27648253	Crystal structure of a monoclonal antibody directed against an antigenic determinant common to Ogawa and Inaba serotypes of Vibrio cholerae O1
Q27631610	Crystal structure of a mutant human lysozyme with a substituted disulfide bond
Q46724996	Crystal structure of a new class of glutathione transferase from the model human hookworm nematode Heligmosomoides polygyrus.
Q91610279	Crystal structure of a novel ATPase RadD from Escherichia coli
Q27653537	Crystal structure of a novel Sm-like protein of putative cyanophage origin at 2.60 Å resolution
Q46589580	Crystal structure of a novel Thermotoga maritima enzyme (TM1112) from the cupin family at 1.83 A resolution
Q27653173	Crystal structure of a novel archaeal AAA+ ATPase SSO1545 fromSulfolobus solfataricus
Q27667949	Crystal structure of a novel dimer form of FlgD from P. aeruginosa PAO1
Q93244716	Crystal structure of a novel fold protein Gp72 from the freshwater cyanophage Mic1
Q44960730	Crystal structure of a novel manganese-containing cupin (TM1459) from Thermotoga maritima at 1.65 A resolution
Q27674967	Crystal structure of a novel mitogen‐activated protein kinase phosphatase, SKRP1
Q27650140	Crystal structure of a novel non-Pfam protein AF1514 from Archeoglobus fulgidus DSM 4304 solved by S-SAD using a Cr X-ray source
Q46304080	Crystal structure of a novel prolidase from Deinococcus radiodurans identifies new subfamily of bacterial prolidases.
Q27644010	Crystal structure of a novel single-stranded DNA binding protein from Mycoplasma pneumoniae
Q41110623	Crystal structure of a novel two domain GH78 family α-rhamnosidase from Klebsiella oxytoca with rhamnose bound.
Q27667347	Crystal structure of a phenol‐coupling P450 monooxygenase involved in teicoplanin biosynthesis
Q44817554	Crystal structure of a phosphoribosylaminoimidazole mutase PurE (TM0446) from Thermotoga maritima at 1.77-A resolution
Q47866942	Crystal structure of a phosphotransacetylase from Streptococcus pyogenes
Q37471248	Crystal structure of a predicted precorrin-8x methylmutase from Thermoplasma acidophilum
Q47596538	Crystal structure of a protein associated with cell division from Mycoplasma pneumoniae (GI: 13508053): a novel fold with a conserved sequence motif
Q68596174	Crystal structure of a protein-toxin alpha 1-purothionin at 2.5A and a comparison with predicted models
Q43018120	Crystal structure of a purine/pyrimidine phosphoribosyltransferase-related protein from Thermus thermophilus HB8.
Q27641532	Crystal structure of a putative CN hydrolase from yeast
Q27651129	Crystal structure of a putative DNA methylase TTHA0409 from Thermus thermophilus HB8
Q35546797	Crystal structure of a putative HTH-type transcriptional regulator yxaF from Bacillus subtilis.
Q44960740	Crystal structure of a putative NADPH-dependent oxidoreductase (GI: 18204011) from mouse at 2.10 A resolution
Q48007177	Crystal structure of a putative PII-like signaling protein (TM0021) from Thermotoga maritima at 2.5 A resolution
Q83957597	Crystal structure of a putative acyl-CoA thioesterase from Xanthomonas campestris (XC229) adopts a tetrameric hotdog fold of epsilongamma mode
Q44855333	Crystal structure of a putative aspartate aminotransferase belonging to subgroup IV.
Q44784471	Crystal structure of a putative glutamine amido transferase (TM1158) from Thermotoga maritima at 1.7 A resolution
Q27650670	Crystal structure of a putative lysostaphin peptidase from Vibrio cholerae
Q27657329	Crystal structure of a putative methylmalonyl-coenzyme A epimerase from Thermoanaerobacter tengcongensis at 2.0 A resolution
Q46214522	Crystal structure of a putative modulator of DNA gyrase (pmbA) from Thermotoga maritima at 1.95 A resolution reveals a new fold
Q28485422	Crystal structure of a putative oxalate decarboxylase (TM1287) from Thermotoga maritima at 1.95 A resolution
Q53657371	Crystal structure of a putative phosphinothricin acetyltransferase (PA4866) from Pseudomonas aeruginosa PAC1.
Q46865795	Crystal structure of a putative pyridoxine 5'-phosphate oxidase (Rv2607) from Mycobacterium tuberculosis
Q27680491	Crystal structure of a putative quorum sensing-regulated protein (PA3611) from the Pseudomonas-specific DUF4146 family
Q27734823	Crystal structure of a recombinant form of the maltodextrin-binding protein carrying an inserted sequence of a B-cell epitope from the preS2 region of hepatitis B virus
Q44910194	Crystal structure of a ribose-5-phosphate isomerase RpiB (TM1080) from Thermotoga maritima at 1.90 A resolution
Q27649047	Crystal structure of a secondary vitamin D3 binding site of milk beta-lactoglobulin
Q56978738	Crystal structure of a single-stranded DNA-binding protein (TM0604) from Thermotoga maritima at 2.60 Å resolution
Q27678402	Crystal structure of a supercharged variant of the human enteropeptidase light chain
Q46320318	Crystal structure of a tandem cystathionine-beta-synthase (CBS) domain protein (TM0935) from Thermotoga maritima at 1.87 A resolution
Q27621093	Crystal structure of a thermophilic alcohol dehydrogenase substrate complex suggests determinants of substrate specificity and thermostability
Q27643664	Crystal structure of a transcription regulator (TM1602) from Thermotoga maritima at 2.3 A resolution
Q27646782	Crystal structure of a transcriptional activator of comK gene from Bacillus halodurans
Q27659695	Crystal structure of a triacylglycerol lipase from Penicillium expansum at 1.3 A determined by sulfur SAD
Q27657330	Crystal structure of a trimeric archaeal adenylate kinase from the mesophile Methanococcus maripaludis with an unusually broad functional range and thermal stability
Q27628955	Crystal structure of a truncated form of porcine odorant-binding protein
Q27663517	Crystal structure of a truncated urease accessory protein UreF from Helicobacter pylori
Q45257277	Crystal structure of a truncated version of the phage lambda protein gpD.
Q46025762	Crystal structure of a type II quinolic acid phosphoribosyltransferase (TM1645) from Thermotoga maritima at 2.50 A resolution.
Q44252320	Crystal structure of a zinc-containing glycerol dehydrogenase (TM0423) from Thermotoga maritima at 1.5 A resolution
Q43559566	Crystal structure of acireductone dioxygenase (ARD) from Mus musculus at 2.06 angstrom resolution
Q27678201	Crystal structure of agkisacucetin, a Gpib-binding snake C-type lectin that inhibits platelet adhesion and aggregation
Q82068613	Crystal structure of alanyl-tRNA synthetase editing-domain homolog (PH0574) from a hyperthermophile, Pyrococcus horikoshii OT3 at 1.45 A resolution
Q27648249	Crystal structure of aminopeptidase N from human pathogen Neisseria meningitidis
Q27649853	Crystal structure of an ADP-ribosylated protein with a cytidine deaminase-like fold, but unknown function (TM1506), from Thermotoga maritima at 2.70 A resolution
Q34431926	Crystal structure of an Apo mRNA decapping enzyme (DcpS) from Mouse at 1.83 A resolution
Q46145171	Crystal structure of an HEPN domain protein (TM0613) from Thermotoga maritima at 1.75 A resolution
Q56978648	Crystal structure of an ORFan protein (TM1622) fromThermotoga maritimaat 1.75 Å resolution reveals a fold similar to the Ran-binding protein Mog1p
Q82585442	Crystal structure of an RtcB homolog protein (PH1602-extein protein) from Pyrococcus horikoshii reveals a novel fold
Q46128390	Crystal structure of an Udp-n-acetylmuramate-alanine ligase MurC (TM0231) from Thermotoga maritima at 2.3 A resolution
Q27646622	Crystal structure of an acetyltransferase protein fromVibrio choleraestrain N16961
Q45229452	Crystal structure of an alanine-glyoxylate aminotransferase from Anabaena sp. at 1.70 A resolution reveals a noncovalently linked PLP cofactor
Q43608572	Crystal structure of an aldehyde reductase Y50F mutant-NADP complex and its implications for substrate binding
Q27652281	Crystal structure of an alkaline serine protease from Nesterenkonia sp. defines a novel family of secreted bacterial proteases
Q34330586	Crystal structure of an allantoicase (YIR029W) from Saccharomyces cerevisiae at 2.4 A resolution
Q44071941	Crystal structure of an alpha/beta serine hydrolase (YDR428C) from Saccharomyces cerevisiae at 1.85 A resolution
Q46721054	Crystal structure of an archaeal Sm protein from Sulfolobus solfataricus.
Q27662227	Crystal structure of an archaeal cleavage and polyadenylation specificity factor subunit from Pyrococcus horikoshii
Q79935373	Crystal structure of an archaeal homologue of multidrug resistance repressor protein, EmrR, from hyperthermophilic archaea Sulfolobus tokodaii strain 7
Q43023614	Crystal structure of an archaeal specific DNA-binding protein (Ape10b2) from Aeropyrum pernix K1.
Q44855358	Crystal structure of an aspartate aminotransferase (TM1255) from Thermotoga maritima at 1.90 A resolution
Q27660234	Crystal structure of an eIF4G-like protein fromDanio rerio
Q56978885	Crystal structure of an indigoidine synthase A (IndA)-like protein (TM1464) from Thermotoga maritima at 1.90 Å resolution reveals a new fold
Q27642900	Crystal structure of an iron-containing 1,3-propanediol dehydrogenase (TM0920) from Thermotoga maritima at 1.3 A resolution
Q46091228	Crystal structure of an orphan protein (TM0875) from Thermotoga maritima at 2.00-A resolution reveals a new fold
Q46848400	Crystal structure of antigen TpF1 from Treponema pallidum
Q27703593	Crystal structure of archaeal ketopantoate reductase complexed with coenzyme a and 2-oxopantoate provides structural insights into feedback regulation
Q27650205	Crystal structure of archaeal tRNA(m(1)G37)methyltransferase aTrm5
Q27662960	Crystal structure of archaemetzincin AmzA from Methanopyrus kandleri at 1.5 A resolution
Q57875907	Crystal structure of axolotl (Ambystoma mexicanum) liver bile acid-binding protein bound to cholic and oleic acid
Q27675746	Crystal structure of bacteriophage ϕNIT1 zinc peptidase PghP that hydrolyzes γ-glutamyl linkage of bacterial poly-γ-glutamate
Q27626597	Crystal structure of bovine duodenase, a serine protease, with dual trypsin and chymotrypsin-like specificities
Q27645355	Crystal structure of calcium binding protein-1 from Entamoeba histolytica: a novel arrangement of EF hand motifs
Q27749440	Crystal structure of calcium-independent subtilisin BPN′ with restored thermal stability folded without the prodomain
Q98161380	Crystal structure of chalcone synthase, a key enzyme for isoflavonoid biosynthesis in soybean
Q27643629	Crystal structure of chemically synthesized vMIP-II
Q56764579	Crystal structure of chloramphenicol acetyltransferase B2 encoded by the multiresistance transposon Tn2424
Q27642898	Crystal structure of chorismate synthase from Aquifex aeolicus reveals a novel beta alpha beta sandwich topology
Q27685221	Crystal structure of conjugated polyketone reductase (CPR-C1) from Candida parapsilosis IFO 0708 complexed with NADPH
Q48007394	Crystal structure of conserved protein PH1136 from Pyrococcus horikoshii.
Q27666119	Crystal structure of curcuminoid synthase CUS from Oryza sativa
Q81528787	Crystal structure of decameric peroxiredoxin (AhpC) from Amphibacillus xylanus
Q27675247	Crystal structure of decaprenylphosphoryl-β-D-ribose 2'-epimerase fromMycobacterium smegmatis
Q80914870	Crystal structure of dehydroquinate synthase from Thermus thermophilus HB8 showing functional importance of the dimeric state
Q27684504	Crystal structure of deltarhodopsin‐3 from Haloterrigena thermotolerans
Q43029698	Crystal structure of dibenzothiophene sulfone monooxygenase BdsA from Bacillus subtilis WU-S2B.
Q46803237	Crystal structure of dihydrodipicolinate synthase (BA3935) from Bacillus anthracis at 1.94 A resolution
Q45729072	Crystal structure of elongation factor P from Pseudomonas aeruginosa at 1.75 å resolution
Q27651672	Crystal structure of engineered beta-glucosidase from a soil metagenome
Q51186372	Crystal structure of fatty acid-CoA racemase from Mycobacterium tuberculosis H37Rv
Q46832312	Crystal structure of flavin binding to FAD synthetase of Thermotoga maritima
Q27642894	Crystal structure of gamma-glutamyl phosphate reductase (TM0293) from Thermotoga maritima at 2.0 A resolution
Q45028395	Crystal structure of gene locus At3g16990 from Arabidopsis thaliana
Q27656419	Crystal structure of ginkbilobin-2 with homology to the extracellular domain of plant cysteine-rich receptor-like kinases
Q27674916	Crystal structure of glucuronic acid dehydrogenase [correction of dehydrogeanse] from Chromohalobacter salexigens
Q27639732	Crystal structure of glutamine amidotransferase fromThermotoga maritima
Q27645350	Crystal structure of glutathione reductase Glr1 from the yeast Saccharomyces cerevisiae
Q27651950	Crystal structure of glutathione-dependent phospholipid peroxidase Hyr1 from the yeast Saccharomyces cerevisiae
Q46848393	Crystal structure of glyceraldehyde-3-phosphate dehydrogenase from Plasmodium falciparum at 2.25 A resolution reveals intriguing extra electron density in the active site.
Q27649609	Crystal structure of glycerophosphodiester phosphodiesterase (GDPD) from Thermoanaerobacter tengcongensis, a metal ion-dependent enzyme: insight into the catalytic mechanism
Q80113383	Crystal structure of glycerophosphodiester phosphodiesterase from Agrobacterium tumefaciens by SAD with a large asymmetric unit
Q39226755	Crystal structure of heart 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase (PFKFB2) and the inhibitory influence of citrate on substrate binding
Q27675741	Crystal structure of homoisocitrate dehydrogenase from Schizosaccharomyces pombe
Q27645233	Crystal structure of homoserine O-succinyltransferase from Bacillus cereus at 2.4 A resolution
Q34645728	Crystal structure of human Ankyrin G death domain
Q44855348	Crystal structure of human L-xylulose reductase holoenzyme: probing the role of Asn107 with site-directed mutagenesis
Q28265727	Crystal structure of human SH3BGRL protein: the first structure of the human SH3BGR family representing a novel class of thioredoxin fold proteins
Q34574153	Crystal structure of human TMDP, a testis-specific dual specificity protein phosphatase: implications for substrate specificity
Q27651133	Crystal structure of human carbonic anhydrase XIII and its complex with the inhibitor acetazolamide
Q27654629	Crystal structure of human carbonic anhydrase-related protein VIII reveals the basis for catalytic silencing
Q27649297	Crystal structure of human cellular retinol-binding protein II to 1.2 A resolution
Q27649296	Crystal structure of human cyclophilin D in complex with its inhibitor, cyclosporin A at 0.96-A resolution
Q27677502	Crystal structure of human cytosolic aspartyl‐tRNA synthetase, a component of multi‐tRNA synthetase complex
Q24311982	Crystal structure of human diphosphoinositol phosphatase 1
Q34577177	Crystal structure of human dual specificity phosphatase, JNK stimulatory phosphatase-1, at 1.5 A resolution
Q27654071	Crystal structure of human eIF5A1: insight into functional similarity of human eIF5A1 and eIF5A2
Q27642167	Crystal structure of human immunoglobulin fragment Fab New refined at 2.0 A resolution
Q38456781	Crystal structure of human multiple copies in T‐cell lymphoma‐1 oncoprotein
Q27643992	Crystal structure of human myo-inositol monophosphatase 2, the product of the putative susceptibility gene for bipolar disorder, schizophrenia, and febrile seizures
Q27648284	Crystal structure of human nucleophosmin-core reveals plasticity of the pentamer-pentamer interface
Q27637712	Crystal structure of human nucleoside diphosphate kinase A, a metastasis suppressor
Q27622554	Crystal structure of human ornithine transcarbamylase complexed with carbamoyl phosphate and L-norvaline at 1.9 A resolution
Q27653392	Crystal structure of human osteoclast stimulating factor
Q48007168	Crystal structure of human p120 homologue protein PH1374 from Pyrococcus horikoshii
Q27651131	Crystal structure of human phosphomevalonate kinase at 1.8 A resolution
Q34501848	Crystal structure of human protein tyrosine phosphatase 14 (PTPN14) at 1.65-A resolution
Q27652880	Crystal structure of human retinoblastoma binding protein 9
Q27644410	Crystal structure of human slingshot phosphatase 2
Q82863243	Crystal structure of human spermidine/spermine N1-acetyltransferase (hSSAT): the first structure of a new sequence family of transferase homologous superfamily
Q27621914	Crystal structure of human ubiquitous mitochondrial creatine kinase
Q80610301	Crystal structure of hypothetical protein PH0642 from Pyrococcus horikoshii at 1.6A resolution
Q27652346	Crystal structure of hypothetical protein PH0734.1 from hyperthermophilic archaea Pyrococcus horikoshii OT3
Q80610309	Crystal structure of hypothetical protein PH0828 from Pyrococcus horikoshii
Q27676667	Crystal structure of hypothetical protein TTHB210, controlled by the σ(E) /anti-σ(E) regulatory system in Thermus thermophilus HB8, reveals a novel homodecamer
Q30437663	Crystal structure of hypothetical protein YfiH from Shigella flexneri at 2 A resolution
Q51264884	Crystal structure of intein homing endonuclease II encoded in DNA polymerase gene from hyperthermophilic archaeon Thermococcus kodakaraensis strain KOD1.
Q27665814	Crystal structure of isoamyl acetate-hydrolyzing esterase from Saccharomyces cerevisiae reveals a novel active site architecture and the basis of substrate specificity
Q44898287	Crystal structure of isocitrate dehydrogenase from Aeropyrum pernix
Q27694799	Crystal structure of juvenile hormone epoxide hydrolase from the silkworm Bombyx mori
Q47995292	Crystal structure of lipoate-bound lipoate ligase 1, LipL1, from Plasmodium falciparum
Q46622877	Crystal structure of methenyltetrahydrofolate synthetase from Mycoplasma pneumoniae (GI: 13508087) at 2.2 A resolution
Q54719164	Crystal structure of myoglobin from a synthetic gene.
Q27667432	Crystal structure of native Anopheles gambiae serpin-2, a negative regulator of melanization in mosquitoes
Q27650107	Crystal structure of native O-acetyl-serine sulfhydrylase from Entamoeba histolytica and its complex with cysteine: structural evidence for cysteine binding and lack of interactions with serine acetyl transferase
Q27652428	Crystal structure of native cinnamomin isoform III and its comparison with other ribosome inactivating proteins
Q27637481	Crystal structure of non-allosteric L-lactate dehydrogenase from Lactobacillus pentosus at 2.3 A resolution: specific interactions at subunit interfaces
Q48020683	Crystal structure of nonspecific lipid transfer protein from Solanum melongena
Q27642899	Crystal structure of osmotin, a plant antifungal protein
Q91163256	Crystal structure of pantoate kinase from Thermococcus kodakarensis
Q45070150	Crystal structure of peptide deformylase from Staphylococcus aureus in complex with actinonin, a naturally occurring antibacterial agent
Q27655519	Crystal structure of phenylacetic acid degradation protein PaaG from Thermus thermophilus HB8
Q79895869	Crystal structure of phosphatidylglycerophosphatase (PGPase), a putative membrane-bound lipid phosphatase, reveals a novel binuclear metal binding site and two "proton wires"
Q27650878	Crystal structure of phosphoglucose isomerase from Trypanosoma brucei complexed with glucose-6-phosphate at 1.6 A resolution
Q27639878	Crystal structure of phosphoglucose isomerase from pig muscle and its complex with 5-phosphoarabinonate
Q27689554	Crystal structure of phosphopantothenate synthetase from Thermococcus kodakarensis
Q46153449	Crystal structure of phosphoribosylformyl-glycinamidine synthase II, PurS subunit (TM1244) from Thermotoga maritima at 1.90 A resolution
Q46181744	Crystal structure of phosphoribosylformylglycinamidine synthase II (smPurL) from Thermotoga maritima at 2.15 A resolution
Q46766771	Crystal structure of putative N-acetyl-gamma-glutamyl-phosphate reductase (AK071544) from rice (Oryza sativa).
Q46898521	Crystal structure of quinolinic acid phosphoribosyltransferase from Helicobacter pylori
Q27644050	Crystal structure of recombinant human stromal cell-derived factor-1alpha
Q27622756	Crystal structure of recombinant trypsin-solubilized fragment of cytochrome b(5) and the structural comparison with Val61His mutant
Q27650071	Crystal structure of single-domain VL of an anti-DNA binding antibody 3D8 scFv and its active site revealed by complex structures of a small molecule and metals
Q52841312	Crystal structure of stilbene synthase from Arachis hypogaea
Q27642258	Crystal structure of tRNA (m1G37) methyltransferase from Aquifex aeolicus at 2.6 Å resolution: A novel methyltransferase fold
Q27678696	Crystal structure of tandem ACT domain-containing protein ACTP from Galdieria sulphuraria
Q47214914	Crystal structure of tetrameric human Rabin8 GEF domain
Q45070173	Crystal structure of the ATP-binding cassette of multisugar transporter from Pyrococcus horikoshii OT3.
Q56978684	Crystal structure of the ApbE protein (TM1553) from Thermotoga maritima at 1.58 Å resolution
Q27653938	Crystal structure of the Bacillus anthracis nucleoside diphosphate kinase and its characterization reveals an enzyme adapted to perform under stress conditions
Q41439174	Crystal structure of the C-terminal 2',5'-phosphodiesterase domain of group A rotavirus protein VP3.
Q27649990	Crystal structure of the C-terminal conserved domain of human GRP, a galectin-related protein, reveals a function mode different from those of galectins
Q27684042	Crystal structure of the C-terminal domain of mouse TLR9
Q84398109	Crystal structure of the C-terminal region of human p97/DAP5
Q46770760	Crystal structure of the C107S/C112S mutant of yeast nuclear 2-Cys peroxiredoxin
Q27642857	Crystal structure of the C67A mutant of isopentenyl diphosphate isomerase complexed with a mechanism-based irreversible inhibitor
Q27673322	Crystal structure of the Campylobacter jejuni Cj0090 protein reveals a novel variant of the immunoglobulin fold among bacterial lipoproteins
Q54495563	Crystal structure of the Co-chaperonin Cpn10 from Thermus thermophilus HB8.
Q27657595	Crystal structure of the DNA gyrase GyrA N-terminal domain fromMycobacterium tuberculosis
Q27652352	Crystal structure of the DUF54 family protein PH1010 from hyperthermophilic archaea Pyrococcus horikoshii OT3
Q27638843	Crystal structure of the Escherichia coli SbmC protein that protects cells from the DNA replication inhibitor microcin B17
Q44601568	Crystal structure of the Escherichia coli Tas protein, an NADP(H)-dependent aldo-keto reductase.
Q27640841	Crystal structure of the Escherichia coli YcdX protein reveals a trinuclear zinc active site
Q27642861	Crystal structure of the Escherichia coli YjiA protein suggests a GTP-dependent regulatory function
Q27638955	Crystal structure of the Escherichia coli glucose-inhibited division protein B (GidB) reveals a methyltransferase fold
Q27638954	Crystal structure of the Escherichia coli shikimate kinase I (AroK) that confers sensitivity to mecillinam
Q27653353	Crystal structure of the Fic (Filamentation induced by cAMP) family protein SO4266 (gi\|24375750) from Shewanella oneidensis MR-1 at 1.6 Å resolution
Q27667079	Crystal structure of the GAF-B domain from human phosphodiesterase 5
Q27648281	Crystal structure of the Helicobacter pylori enoyl-acyl carrier protein reductase in complex with hydroxydiphenyl ether compounds, triclosan and diclosan
Q27678456	Crystal structure of the Kar3-like kinesin motor domain from the filamentous fungus Ashbya gossypii
Q47380035	Crystal structure of the Legionella effector Lem22.
Q36469768	Crystal structure of the Legionella pneumophila Lem10 effector reveals a new member of the HD protein superfamily
Q57662978	Crystal structure of the MYB domain of the RAD transcription factor from Antirrhinum majus
Q27658771	Crystal structure of the MukB hinge domain with coiled-coil stretches and its functional implications
Q27689464	Crystal structure of the Mycobacterium tuberculosis phosphate binding protein PstS3
Q27678865	Crystal structure of the N-terminal domain of EccA₁ ATPase from the ESX-1 secretion system of Mycobacterium tuberculosis.
Q27709756	Crystal structure of the N-terminal domain of human SIRT7 reveals a three-helical domain architecture
Q27687165	Crystal structure of the N-terminal methyltransferase-like domain of anamorsin
Q27679327	Crystal structure of the O intermediate of the Leu93→Ala mutant of bacteriorhodopsin
Q27649289	Crystal structure of the PH1932 protein, a unique archaeal ArsR type winged-HTH transcription factor from Pyrococcus horikoshii OT3
Q27645446	Crystal structure of the PIN domain of human telomerase-associated protein EST1A
Q27701665	Crystal structure of the PepSY-containing domain of the YpeB protein involved in germination of bacillus spores
Q27677394	Crystal structure of the S187F variant of human liver alanine: Aminotransferase associated with primary hyperoxaluria type I and its functional implications
Q27638956	Crystal structure of the Streptococcus pneumoniae phosphomevalonate kinase, a member of the GHMP kinase superfamily
Q27678121	Crystal structure of the TLDc domain of oxidation resistance protein 2 from zebrafish
Q47430783	Crystal structure of the TM1442 protein from Thermotoga maritima, a homolog of the Bacillus subtilis general stress response anti-anti-sigma factor RsbV.
Q71074646	Crystal structure of the Trypanosoma cruzi trypanothione reductase.mepacrine complex
Q27937236	Crystal structure of the YGR205w protein from Saccharomyces cerevisiae: close structural resemblance to E. coli pantothenate kinase
Q27639585	Crystal structure of the YciO protein from Escherichia coli
Q34375723	Crystal structure of the YgfY from Escherichia coli, a protein that may be involved in transcriptional regulation
Q27639346	Crystal structure of the YjeE protein from Haemophilus influenzae: a putative Atpase involved in cell wall synthesis
Q81564262	Crystal structure of the YjgF/YER057c/UK114 family protein from the hyperthermophilic archaeon Sulfolobus tokodaii strain 7
Q53594959	Crystal structure of the apo form of D-alanine: D-alanine ligase (Ddl) from Thermus caldophilus: a basis for the substrate-induced conformational changes
Q45964968	Crystal structure of the archaeosine synthase QueF-like-Insights into amidino transfer and tRNA recognition by the tunnel fold.
Q43415087	Crystal structure of the binary complex of pig muscle phosphoglycerate kinase and its substrate 3-phospho-D-glycerate
Q27648234	Crystal structure of the biotin carboxylase domain of human acetyl-CoA carboxylase 2
Q27666556	Crystal structure of the carbon monoxide complex of human cytoglobin
Q27667774	Crystal structure of the catalytic domain of cholesterol‐α‐glucosyltransferase from Helicobacter pylori
Q28271499	Crystal structure of the catalytic domain of human DUSP5, a dual specificity MAP kinase protein phosphatase
Q27655364	Crystal structure of the catalytic domain of human MKP-2 reveals a 24-mer assembly
Q34452031	Crystal structure of the catalytic domain of human VHY, a dual-specificity protein phosphatase
Q27649213	Crystal structure of the catalytic trimer of Methanococcus jannaschii aspartate transcarbamoylase
Q27678125	Crystal structure of the cataract-causing P23T γD-crystallin mutant
Q92926906	Crystal structure of the coiled-coil domain of Drosophila TRIM protein Brat
Q27731522	Crystal structure of the complex of human alpha-thrombin and nonhydrolyzable bifunctional inhibitors, hirutonin-2 and hirutonin-6
Q80202099	Crystal structure of the conserved hypothetical cytosolic protein Xcc0516 from Xanthomonas campestris reveals a novel quaternary structure assembled by five four-helix bundles
Q46333683	Crystal structure of the conserved hypothetical protein MPN330 (GI: 1674200) from Mycoplasma pneumoniae
Q47714884	Crystal structure of the conserved hypothetical protein TT1380 from Thermus thermophilus HB8.
Q27654410	Crystal structure of the conserved hypothetical protein TTHA1606 from Thermus thermophilus HB8
Q54493853	Crystal structure of the copper homeostasis protein (CutCm) from Shigella flexneri at 1.7 A resolution: the first structure of a new sequence family of TIM barrels.
Q27655401	Crystal structure of the cytosolic domain of the cation diffusion facilitator family protein
Q27704012	Crystal structure of the deglycating enzyme Amadoriase I in its free form and substrate-bound complex
Q79152356	Crystal structure of the diadenosine tetraphosphate hydrolase from Shigella flexneri 2a
Q27666109	Crystal structure of the dimeric Oct6 (POU3f1) POU domain bound to palindromic MORE DNA
Q27649815	Crystal structure of the dimeric Urm1 from the yeast Saccharomyces cerevisiae
Q27653393	Crystal structure of the dimerization domain of human filamin A
Q27757639	Crystal structure of the disulfide-stabilized Fv fragment of anticancer antibody B1: Conformational influence of an engineered disulfide bond
Q27648230	Crystal structure of the endopolygalacturonase from the phytopathogenic fungus Colletotrichum lupini and its interaction with polygalacturonase-inhibiting proteins
Q27674730	Crystal structure of the extracellular domain of human myelin protein zero
Q45220732	Crystal structure of the ferredoxin component of carbazole 1,9a-dioxygenase of Pseudomonas resinovorans strain CA10, a novel Rieske non-heme iron oxygenase system
Q27647659	Crystal structure of the flavin reductase component (HpaC) of 4-hydroxyphenylacetate 3-monooxygenase from Thermus thermophilus HB8: Structural basis for the flavin affinity
Q46462376	Crystal structure of the global regulatory protein CsrA from Pseudomonas putida at 2.05 A resolution reveals a new fold
Q27651944	Crystal structure of the hexamer of human heat shock factor binding protein 1
Q27700040	Crystal structure of the human odorant binding protein, OBPIIa
Q51339228	Crystal structure of the hypothetical protein ST2072 from Sulfolobus tokodaii.
Q57895021	Crystal structure of the hypothetical protein TTHA1013 from Thermus thermophilus HB8
Q27684358	Crystal structure of the invertebrate bifunctional purine biosynthesis enzyme PAICS at 2.8 Å resolution
Q102202444	Crystal structure of the large subunit of cobaltochelatase from Mycobacterium tuberculosis
Q27648692	Crystal structure of the leucine zipper domain of small-conductance Ca2+-activated K+ (SK(Ca)) channel from Rattus norvegicus
Q27652878	Crystal structure of the ligand-binding domain of the retinoid X receptor from the ascidian Polyandrocarpa misakiensis
Q27657134	Crystal structure of the manganese transport regulatory protein from Escherichia coli
Q45741815	Crystal structure of the methyltransferase domain of human TARBP1.
Q27648242	Crystal structure of the mouse p53 core domain in zinc-free state
Q27662223	Crystal structure of the noncompetitive xylanase inhibitor TLXI, member of the small thaumatin-like protein family
Q27668134	Crystal structure of the novel PaiA N-acetyltransferase from Thermoplasma acidophilum involved in the negative control of sporulation and degradative enzyme production
Q27668133	Crystal structure of the novel PaiB transcriptional regulator from Geobacillus stearothermophilus
Q27649476	Crystal structure of the proline iminopeptidase-related protein TTHA1809 from Thermus thermophilus HB8
Q36220331	Crystal structure of the protein At3g01520, a eukaryotic universal stress protein-like protein from Arabidopsis thaliana in complex with AMP.
Q35618676	Crystal structure of the protein from Arabidopsis thaliana gene At5g06450, a putative DnaQ‐like exonuclease domain‐containing protein with homohexameric assembly
Q63351984	Crystal structure of the protein from gene At3g17210 of Arabidopsis thaliana
Q46770752	Crystal structure of the putative RNA methyltransferase PH1948 from Pyrococcus horikoshii, in complex with the copurified S-adenosyl-L-homocysteine
Q27650420	Crystal structure of the putative carbohydrate recognition domain of human galectin-related protein
Q83300257	Crystal structure of the pyrimidine 5′‐nucleotidase SDT1 from Saccharomyces cerevisiae complexed with uridine 5′‐monophosphate provides further insight into ligand binding
Q67562110	Crystal structure of the reduced form of p-hydroxybenzoate hydroxylase refined at 2.3 A resolution
Q27690283	Crystal structure of the secreted protein HP1454 from the human pathogen Helicobacter pylori
Q48095709	Crystal structure of the sensor domain of BaeS from Serratia marcescens FS14.
Q57894846	Crystal structure of the single-domain rhodanese homologue TTHA0613 from Thermus thermophilus HB8
Q81394706	Crystal structure of the small form of glucose-inhibited division protein A from Thermus thermophilus HB8
Q27645364	Crystal structure of the tRNA-specific adenosine deaminase from Streptococcus pyogenes
Q27641381	Crystal structure of the type II 3-dehydroquinase from Helicobacter pylori
Q27667516	Crystal structure of the unliganded retinoblastoma protein pocket domain
Q79252707	Crystal structure of the yeast cytoplasmic thioredoxin Trx2
Q27683595	Crystal structure of the ω-aminotransferase from Paracoccus denitrificans and its phylogenetic relationship with other class III aminotransferases that have biotechnological potential
Q27645436	Crystal structure of thioredoxin domain of ST2123 from thermophilic archaea Sulfolobus tokodaii strain7
Q58051288	Crystal structure of thioredoxin peroxidase from aerobic hyperthermophilic archaeon Aeropyrum pernix K1
Q46184015	Crystal structure of thy1, a thymidylate synthase complementing protein from Thermotoga maritima at 2.25 A resolution
Q27704006	Crystal structure of translation initiation factor 5B from the crenarchaeon Aeropyrum pernix
Q27621082	Crystal structure of tropomyosin at 7 Angstroms resolution
Q27651931	Crystal structure of ultralente--a microcrystalline insulin suspension
Q27650069	Crystal structure of uncharacterized protein TTHA1756 from Thermus thermophilus HB8: Structural variety in UPF0150 family proteins
Q28487284	Crystal structure of uncleaved L-aspartate-alpha-decarboxylase from Mycobacterium tuberculosis
Q46661972	Crystal structure of ureidoglycolate hydrolase (AllA) from Escherichia coli O157:H7.
Q27641922	Crystal structure of uronate isomerase (TM0064) from Thermotoga maritima at 2.85 A resolution
Q46221648	Crystal structure of virulence factor CJ0248 from Campylobacter jejuni at 2.25 A resolution reveals a new fold
Q27649818	Crystal structure of yeast hexokinase PI in complex with glucose: A classical "induced fit" example revised
Q48136600	Crystal structure of yeast nitronate monooxygenase from Cyberlindnera saturnus.
Q38289229	Crystal structure of β-glucosidase 1A from Thermotoga neapolitana and comparison of active site mutants for hydrolysis of flavonoid glucosides
Q27639348	Crystal structure ofEscherichia coli EC1530, a glyoxylate induced protein YgbM
Q80867966	Crystal structure solution of a ParB-like nuclease at atomic resolution
Q27748895	Crystal structures and properties of de novo circularly permuted 1,3-1,4-β-glucanases
Q54454409	Crystal structures of E. coli CcmG and its mutants reveal key roles of the N-terminal beta-sheet and the fingerprint region.
Q27765349	Crystal structures of HLA-A*0201 complexed with antigenic peptides with either the amino- or carboxyl-terminal group substituted by a methyl group
Q27684357	Crystal structures of Klebsiella pneumoniae pantothenate kinase in complex with N‐substituted pantothenamides
Q27657332	Crystal structures of Lys-63-linked tri- and di-ubiquitin reveal a highly extended chain architecture
Q27641687	Crystal structures of MTH1187 and its yeast ortholog YBL001c
Q27650015	Crystal structures of MW1337R and lin2004: representatives of a novel protein family that adopt a four-helical bundle fold
Q27704185	Crystal structures of OprN and OprJ, outer membrane factors of multidrug tripartite efflux pumps of Pseudomonas aeruginosa
Q27648494	Crystal structures of Salmonella typhimurium propionate kinase and its complex with Ap4A: evidence for a novel Ap4A synthetic activity
Q44960735	Crystal structures of Staphylococcus aureus type I dehydroquinase from enzyme turnover experiments
Q27666633	Crystal structures of a family 8 polysaccharide lyase reveal open and highly occluded substrate-binding cleft conformations
Q114873201	Crystal structures of a new class of pyrimidine/purine nucleoside phosphorylase revealed a Cupin fold
Q27640466	Crystal structures of a psychrophilic metalloprotease reveal new insights into catalysis by cold-adapted proteases
Q27688898	Crystal structures of carbohydrate recognition domain of blood dendritic cell antigen-2 (BDCA2) reveal a common domain-swapped dimer
Q27642256	Crystal structures of ferrous horse heart myoglobin complexed with nitric oxide and nitrosoethane
Q27702223	Crystal structures of halohydrin hydrogen-halide-lyases from Corynebacterium sp. N-1074
Q27660308	Crystal structures of holo and Cu-deficient Cu/Zn-SOD from the silkworm Bombyx mori and the implications in amyotrophic lateral sclerosis
Q84025507	Crystal structures of human CDY proteins reveal a crotonase-like fold
Q34542476	Crystal structures of human sulfotransferases SULT1B1 and SULT1C1 complexed with the cofactor product adenosine-3'- 5'-diphosphate (PAP).
Q27684067	Crystal structures of ligand-bound octaprenyl pyrophosphate synthase fromEscherichia colireveal the catalytic and chain-length determining mechanisms
Q27687066	Crystal structures of starch binding domain from Rhizopus oryzae glucoamylase in complex with isomaltooligosaccharide: insights into polysaccharide binding mechanism of CBM21 family
Q46955007	Crystal structures of subtilisin BPN' variants containing disulfide bonds and cavities: concerted structural rearrangements induced by mutagenesis
Q27650645	Crystal structures of the Mycobacterium tuberculosis secretory antigen alanine dehydrogenase (Rv2780) in apo and ternary complex forms captures "open" and "closed" enzyme conformations
Q80072844	Crystal structures of the PLP- and PMP-bound forms of BtrR, a dual functional aminotransferase involved in butirosin biosynthesis
Q43000312	Crystal structures of the apo and GDP-bound forms of a cupin-like protein BbDUF985 from Branchiostoma belcheri tsingtauense
Q27689000	Crystal structures of the archaeal UDP-GlcNAc 2-epimerase from Methanocaldococcus jannaschii reveal a conformational change induced by UDP-GlcNAc
Q83096037	Crystal structures of the complexes of a group IIA phospholipase A2 with two natural anti-inflammatory agents, anisic acid, and atropine reveal a similar mode of binding
Q27621908	Crystal structures of the complexes of trichosanthin with four substrate analogs and catalytic mechanism of RNA N-glycosidase
Q27745648	Crystal structures of the methane monooxygenase hydroxylase from Methylococcus capsulatus (Bath): Implications for substrate gating and component interactions
Q27631038	Crystal structures of the peanut lectin-lactose complex at acidic pH: retention of unusual quaternary structure, empty and carbohydrate bound combining sites, molecular mimicry and crystal packing directed by interactions at the combining site
Q27732113	Crystal structures of two mutants of adenylate kinase from Escherichia coli that modify the Gly-loop
Q27646874	Crystal structures of two novel dye-decolorizing peroxidases reveal a beta-barrel fold with a conserved heme-binding motif
Q35585795	Crystal structures of two putative phosphoheptose isomerases.
Q27639583	Crystal structures of unligated and CN-ligated Glycera dibranchiata monomer ferric hemoglobin components III and IV
Q30159617	Crystal structures of vegetative soybean lipoxygenase VLX-B and VLX-D, and comparisons with seed isoforms LOX-1 and LOX-3
Q27765159	Crystal structures ofBacillus stearothermophilus adenylate kinase with bound Ap5A, Mg2+ Ap5A, and Mn2+ Ap5A reveal an intermediate lid position and six coordinate octahedral geometry for bound Mg2+ and Mn2+
Q71374377	Crystallization and X-ray analysis of a single fab binding domain from protein L of Peptostreptococcus magnus
Q36788614	Crystallization and X-ray diffraction data of the cleaved form of plasminogen activator inhibitor-1.
Q54632307	Crystallization and characterization of colicin E1 channel-forming polypeptides.
Q72521332	Crystallization and characterization of the recombinant human Clara cell 10-kDa protein
Q54589416	Crystallization and preliminary X-ray analysis of Escherichia coli methionyl-tRNA(fMet) formyltransferase.
Q41113837	Crystallization and preliminary X-ray analysis of Escherichia coli peptidyl-tRNA hydrolase.
Q71565984	Crystallization and preliminary X-ray analysis of Pit-1 POU domain complexed to a 28 base pair DNA element
Q60238375	Crystallization and preliminary X-ray analysis of nonglycosylated tissue inhibitor of metalloproteinases-1, N30QN78Q TIMP-1
Q54592604	Crystallization and preliminary X-ray analysis of the Escherichia coli replication terminator protein complexed with DNA.
Q53057369	Crystallization and preliminary X-ray analysis of the cytoplasmic domain of human erythrocyte band 3.
Q34425126	Crystallization and preliminary X-ray analysis of the flavoenzyme vanillyl-alcohol oxidase from Penicillium simplicissimum.
Q43024140	Crystallization and preliminary X-ray characterization of the Methanothermus fervidus histones HMfA and HMfB.
Q71374345	Crystallization and preliminary X-ray crystallographic analysis of ImmE7 protein of colicin E7
Q70581316	Crystallization and preliminary X-ray crystallographic analysis of arylesterase from Pseudomonas fluorescens
Q72589774	Crystallization and preliminary X-ray crystallographic analysis of chitinase from barley seeds
Q72141155	Crystallization and preliminary X-ray crystallographic analysis of phospholipid transfer protein from maize seedlings
Q71537038	Crystallization and preliminary X-ray crystallographic studies of nonhistone region of macroH2A.1.
Q54587474	Crystallization and preliminary X-ray crystallographic studies of recombinant bovine neurocalcin delta.
Q73134830	Crystallization and preliminary X-ray crystallographic study of the Ras-GTPase-activating domain of human p120GAP
Q59287379	Crystallization and preliminary X-ray diffraction analysis of bovine seminal plasma PDC-109, a protein composed of two fibronectin type II domains
Q68188225	Crystallization and preliminary X-ray diffraction analysis of staphylococcal enterotoxin type C
Q36866181	Crystallization and preliminary X-ray diffraction data of two different human low-density lipoprotein (LDL) subfractions
Q36783292	Crystallization and preliminary X-ray diffraction data of two heparin-binding fragments of human fibronectin
Q71763583	Crystallization and preliminary X-ray diffraction studies of a bacterial flavohemoglobin protein
Q45778849	Crystallization and preliminary X-ray diffraction studies of a monoclonal antibody Fab fragment against foot-and-mouth disease virus and of its complex with the main antigenic site peptide
Q58375385	Crystallization and preliminary X-ray diffraction studies of an a1/α2/DNA ternary complex
Q70830914	Crystallization and preliminary X-ray diffraction studies of complexes between an influenza hemagglutinin and Fab fragments of two different monoclonal antibodies
Q64949822	Crystallization and preliminary X-ray diffraction studies of dogfish C-reactive protein.
Q71705248	Crystallization and preliminary X-ray diffraction studies of formylmethanofuran: tetrahydromethanopterin formyltransferase from Methanopyrus kandleri
Q64038879	Crystallization and preliminary X-ray diffraction studies of human procathepsin L
Q67777646	Crystallization and preliminary X-ray diffraction studies of human salivary alpha-amylase
Q72867745	Crystallization and preliminary X-ray diffraction studies of mandelonitrile lyase from almonds
Q72952943	Crystallization and preliminary X-ray diffraction studies of peroxidase from a fungus Arthromyces ramosus
Q41646372	Crystallization and preliminary X-ray diffraction studies of the human major histocompatibility antigen HLA-B27
Q44964300	Crystallization and preliminary X-ray diffraction studies of two mutants of lactate dehydrogenase from Bacillus stearothermophilus
Q57396080	Crystallization and preliminary X-ray diffraction study of 1,3,8-trihydroxynaphthalene reductase fromMagnaporthe grisea
Q68085496	Crystallization and preliminary X-ray diffraction study of a protein with a high potential rubredoxin center and a hemerythrin-type Fe center
Q58072266	Crystallization and preliminary X-ray diffraction study of the green flavoenzyme 5-Hydroxyvaleryl-CoA dehydratase/dehydrogenase from Clostridium aminovalericum
Q54577824	Crystallization and preliminary X-ray investigation at 2.0 A resolution of Bet v 1, a birch pollen protein causing IgE-mediated allergy.
Q62083044	Crystallization and preliminary X-ray investigation of a recombinant form of rat catecholO-methyltransferase
Q54648635	Crystallization and preliminary X-ray investigation of barstar, the intracellular inhibitor of barnase.
Q71763604	Crystallization and preliminary X-ray investigation of recombinant human interleukin 10
Q57922414	Crystallization and preliminary X-ray investigation of the recombinant Trypanosoma brucei rhodesiense calmodulin
Q54484741	Crystallization and preliminary X-ray studies of I-CreI: a group I intron-encoded endonuclease from C. reinhardtii.
Q71565991	Crystallization and preliminary X-ray studies of ornithine decarboxylase from Trypanosoma brucei
Q72061295	Crystallization and preliminary X‐ray diffraction studies of leishmanolysin, the major surface metalloproteinase from Leishmania major
Q72061299	Crystallization and preliminary X‐ray diffraction studies of the cartilage link protein from bovine trachea
Q68262403	Crystallization and preliminary analysis of enzyme-substrate complexes of pyruvate kinase from rabbit muscle
Q48048063	Crystallization and preliminary cryogenic X-ray diffraction analyses of protein L-isoaspartylO-methyltransferase from human fetal brain
Q54589419	Crystallization and preliminary crystallographic analysis of RepA1, a replication control protein of the RepFIC replicon of enterotoxin plasmid EntP307.
Q71537033	Crystallization and preliminary crystallographic analysis of a 2,3-dihydroxybiphenyl dioxygenase from Pseudomonas sp. strain KKS102 having polychlorinated biphenyl (PCB)-degrading activity
Q71374355	Crystallization and preliminary crystallographic analysis of an amylopullulanase from the hyperthermophilic archaeon Pyrococcus woesei
Q70830926	Crystallization and preliminary crystallographic analysis of recombinant abrin-a A-chain with ribosome inactivating activity
Q72957334	Crystallization and preliminary crystallographic analysis of ribonuclease H from Thermus thermophilus HB8
Q73134822	Crystallization and preliminary crystallographic analysis of ribosomal protein S8 from Thermus thermophilus
Q54581756	Crystallization and preliminary crystallographic analysis of tetrahydrodipicolinate-N-succinyltransferase.
Q73510598	Crystallization and preliminary crystallographic analysis of the N-terminal actin binding domain of human fimbrin
Q71681048	Crystallization and preliminary crystallographic analysis of the N-terminal two domain fragment of vascular cell adhesion molecule-1 (VCAM-1)
Q36694724	Crystallization and preliminary crystallographic data for class I deoxyribose‐5‐phosphate aldolase fromEscherichia coli: An Application of Reverse Screening
Q36847094	Crystallization and preliminary crystallographic data of a neutrophil migration-inducing lectin (KM+) extracted from the seed of Artocarpus integrifolia
Q59651728	Crystallization and preliminary crystallographic data of a neutrophil migration-inducing lectin (KM+) extracted from the seed ofArtocarpus integrifolia
Q30468988	Crystallization and preliminary crystallographic studies of 3-deoxy-D-manno-octulosonate-8-phosphate synthase from Escherichia coli
Q72511037	Crystallization and preliminary crystallographic studies of the precursor and mature forms of a neutral lipase from the fungus Rhizopus delemar
Q72154723	Crystallization and preliminary crystallographic study of human CksHs1: a cell cycle regulatory protein
Q57225272	Crystallization and preliminary crystallographic study of human lithostathine
Q71565977	Crystallization and preliminary crystallographic study of the pentamerizing domain from cartilage oligomeric matrix protein: a five-stranded alpha-helical bundle
Q42549662	Crystallization and preliminary diffraction analysis of Ca(2+)-calmodulin-drug and apocalmodulin-drug complexes
Q46206441	Crystallization and preliminary diffraction studies of thioesterase II from rat mammary gland
Q54757151	Crystallization and preliminary investigation of single crystals of deoxyuridine triphosphate nucleotidohydrolase from Escherichia coli.
Q46825512	Crystallization and preliminary structural studies of a chorismate mutase catalytic antibody complexed with a transition state analog
Q46216642	Crystallization and preliminary structural studies of the ncd motor domain
Q73134827	Crystallization and preliminary studies of lima bean trypsin inhibitor
Q73083616	Crystallization and preliminary x-ray analysis of recombinant staphylokinase
Q71074639	Crystallization and preliminary x-ray analysis of volvatoxin A2 from Volvariella volvacea
Q71660319	Crystallization and preliminary x-ray crystallographic studies of L-2-haloacid dehalogenase from Pseudomonas sp. YL
Q71660308	Crystallization and preliminary x-ray crystallographic studies of ketosteroid isomerase from Pseudomonas putida biotype B
Q46295644	Crystallization and structural analysis of bullfrog red cell L-subunit ferritins
Q71074636	Crystallization of ADP-ribosyl cyclase from Aplysia californica
Q71774376	Crystallization of NAD+ synthetase from Bacillus subtilis
Q58360785	Crystallization of Thermus thermophilus histidyl-tRNA synthetase and Its complex with tRNAHis
Q54611637	Crystallization of UDP-N-acetylglucosamine O-acyltransferase from Escherichia coli.
Q54589423	Crystallization of a family 8 cellulase from Clostridium thermocellum.
Q54634170	Crystallization of a fragment of human fibronectin: introduction of methionine by site-directed mutagenesis to allow phasing via selenomethionine.
Q71565987	Crystallization of a mammalian ornithine decarboxylase
Q52547275	Crystallization of a membrane pore-forming protein with mosquitocidal activity from Bacillus thuringiensis subspecies kyushuensis
Q72867739	Crystallization of a scRIP-gelonin isolated from plant seeds Gelonium multiforum
Q70830922	Crystallization of a soluble, catalytically active form of Escherichia coli leader peptidase
Q72200803	Crystallization of an enzyme-inhibitor complex: proteinase K with its protein inhibitor, PK13
Q71074634	Crystallization of glycosylated and nonglycosylated phytohemagglutinin-L
Q61919933	Crystallization of glycosylated and nonglycosylated phytohemagglutinin‐L
Q45998860	Crystallization of intact monoclonal antibodies.
Q69833446	Crystallization of purified recombinant human interleukin-1 beta
Q71961412	Crystallization of the NAD-dependent 5,10-methylenetetrahydrofolate dehydrogenase from Saccharomyces cerevisiae
Q54561341	Crystallization of the RNA-binding domain of the transcriptional antiterminator protein sacy from Bacillus subtilis
Q71961407	Crystallization of the bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase domain of the human trifunctional enzyme
Q71374350	Crystallization of the complex of human IFN-gamma and the extracellular domain of the IFN-gamma receptor
Q71671465	Crystallization of the purine salvage enzyme adenine phosphoribosyltransferase
Q72635017	Crystallization of the reaction center from Rhodobacter sphaeroides in a new tetragonal form
Q46095608	Crystallization of the receptor binding domain of vascular endothelial growth factor
Q70125487	Crystallization of yeast orotidine 5'-monophosphate decarboxylase complexed with 1-(5'-phospho-beta-D-ribofuranosyl) barbituric acid
Q44395892	Crystallization studies of glycosylated and unglycosylated human recombinant interleukin-2.
Q57563297	Crystallization, characterization, and preliminary crystallographic studies of mitochondrial carbamoyl phosphate synthetase I ofRana catesbeiana
Q27730265	Crystallization, molecular replacement solution, and refinement of tetrameric beta-amylase from sweet potato
Q58483648	Crystallization, preliminary X-ray diffraction study, and crystal packing of a complex between anti-Hen lysozyme antibody F9.13.7 and Guinea-fowl lysozyme
Q30873768	Crystallization, sequence, and preliminary crystallographic data for an antipeptide Fab 50.1 and peptide complexes with the principal neutralizing determinant of HIV-1 gp120
Q27732114	Crystallographic analysis of Thr-200-->His human carbonic anhydrase II and its complex with the substrate, HCO3-
Q27641921	Crystallographic analysis of an "anticalin" with tailored specificity for fluorescein reveals high structural plasticity of the lipocalin loop region
Q39032586	Crystallographic analysis of murine p24γ2 Golgi dynamics domain.
Q27730786	Crystallographic analysis of oxygenated and deoxygenated states of arthropod hemocyanin shows unusual differences
Q70628255	Crystallographic analysis of the interaction between cyclosporin A and the Fab fragment of a monoclonal antibody
Q27655404	Crystallographic and activity-based evidence for thumb flexibility and its relevance in glycoside hydrolase family 11 xylanases
Q27649145	Crystallographic and computational studies on 4-phenyl-N-(beta-D-glucopyranosyl)-1H-1,2,3-triazole-1-acetamide, an inhibitor of glycogen phosphorylase: comparison with alpha-D-glucose, N-acetyl-beta-D-glucopyranosylamine and [...]
Q27658669	Crystallographic and mass spectrometric analyses of a tandem GNAT protein from the clavulanic acid biosynthesis pathway
Q27667788	Crystallographic and microcalorimetric analyses reveal the structural basis for high arginine specificity in the Salmonella enterica serovar Typhimurium periplasmic binding protein STM4351
Q27685190	Crystallographic and mutational analyses of tannase from Lactobacillus plantarum
Q27684090	Crystallographic and mutational studies on the tRNA thiouridine synthetase TtuA
Q53956963	Crystallographic and spectroscopic characterization of a molecular hinge: conformational changes in bothropstoxin I, a dimeric Lys49-phospholipase A2 homologue.
Q27638991	Crystallographic dissection of the thermal motion of protein-sugar complex
Q27676232	Crystallographic refinement of human serum retinol binding protein at 2A resolution
Q27652309	Crystallographic refinement of ricin to 2.5 A
Q68033370	Crystallographic structure analysis of lamprey hemoglobin from anomalous dispersion of synchrotron radiation
Q27733278	Crystallographic structure of metal-free concanavalin A at 2.5 A resolution
Q48090791	Crystallographic studies and primary structure of the antitumor monoclonal CC49 Fab'.
Q45070138	Crystallographic studies of V44 mutants of Clostridium pasteurianum rubredoxin: effects of side-chain size on reduction potential
Q24296920	Crystallographic studies of inhibitor binding sites in human carbonic anhydrase II: a pentacoordinated binding of the SCN- ion to the zinc at high pH
Q27643991	Crystallographic, thermodynamic, and molecular modeling studies of the mode of binding of oligosaccharides to the potent antiviral protein griffithsin
Q50116024	Crystals of an antibody Fv fragment against an integral membrane protein diffracting to 1.28 A resolution
Q73598267	Crystals of cytochrome c-553 from Bacillus pasteurii show diffraction to 0.97 A resolution
Q43875253	Cu(II)-binding properties of a cytochrome c with a synthetic metal-binding site: His-X3-His in an alpha-helix
Q95650577	Cumulative hydropathic topology of a voltage-gated sodium channel at atomic resolution
Q46848922	Curious structure in "canonical" alanine-based peptides
Q30386093	Current status of membrane protein structure classification.
Q31913262	Cutinase unfolding and stabilization by trehalose and mannosylglycerate
Q59592111	Cutinase unfolding and stabilization by trehalose and mannosylglycerate
Q50752193	Cy-preds: An algorithm and a web service for the analysis and prediction of cysteine reactivity
Q46509418	CyClus: a fast, comprehensive cylindrical interface approximation clustering/reranking method for rigid-body protein-protein docking decoys
Q72511030	Cyanomet human hemoglobin crystallized under physiological conditions exhibits the Y quaternary structure
Q114234880	Cyclic Cystine Knot and its Strong Implication on the Structure and Dynamics of Cyclotides
Q44125138	Cys(x)His(y)-Zn2+ interactions: thiol vs. thiolate coordination
Q27649294	Cysteine 10 is critical for the activity of Ochrobactrum anthropi glutathione transferase and its mutation to alanine causes the preferential binding of glutathione to the H-site
Q71565965	Cysteine-191 in aspartate aminotransferases appears to be conserved due to the lack of a neutral mutation pathway to the functional equivalent, alanine-191
Q24610829	Cytosolic domain of the human mitochondrial fission protein fis1 adopts a TPR fold
Q30363672	Cytotoxicity of the Vibrio vulnificus MARTX toxin effector DUF5 is linked to the C2A subdomain.
Q44309134	D-amino acid residues in peptides and proteins.
Q38315065	D-trehalose/D-maltose-binding protein from the hyperthermophilic archaeon Thermococcus litoralis: the binding of trehalose and maltose results in different protein conformational states.
Q51644649	DARWIN: a program for docking flexible molecules
Q45959136	DNABind: A hybrid algorithm for structure-based prediction of DNA-binding residues by combining machine learning- and template-based approaches
Q99204523	DNSS2: improved ab initio protein secondary structure prediction using advanced deep learning architectures
Q33297368	DOCKGROUND system of databases for protein recognition studies: unbound structures for docking
Q30342106	DPANN: improved sequence to structure alignments following fold recognition.
Q47715301	DRESS: a database of REfined solution NMR structures.
Q91793594	DRoP: Automated detection of conserved solvent-binding sites on proteins
Q50642290	Dark proteins: effect of inclusion body formation on quantification of protein expression
Q30799802	Data mining crystallization databases: knowledge-based approaches to optimize protein crystal screens
Q30742612	Data mining the protein data bank: residue interactions
Q48042492	Data-assisted protein structure modeling by global optimization in CASP12.
Q30917020	Data-based model and parameter evaluation in dynamic transcriptional regulatory networks
Q30992986	Data-driven docking: HADDOCK's adventures in CAPRI.
Q30667051	Data-driven models for protein interaction and design.
Q46661990	Database for three dimensional structures of pepsin-like enzymes using the internal coordinate system
Q29614393	Database of homology-derived protein structures and the structural meaning of sequence alignment
Q52881713	Database of protein complexes with multivalent binding ability: Bival-Bind
Q48637921	David Blow (1931-2004).
Q33739863	De novo backbone scaffolds for protein design
Q33416529	De novo identification of binding sequences for antibody replacement molecules
Q44759261	De novo inference of protein function from coarse-grained dynamics.
Q43809337	De novo ligand design to an ensemble of protein structures
Q30403052	De novo protein structure prediction by dynamic fragment assembly and conformational space annealing
Q30419532	Dead-end elimination with perturbations (DEEPer): a provable protein design algorithm with continuous sidechain and backbone flexibility
Q56999368	Deciphering a novel thioredoxin-like fold family
Q38762026	Deciphering common recognition principles of nucleoside mono/di and tri-phosphates binding in diverse proteins via structural matching of their binding sites.
Q47821476	Deciphering the promiscuous interactions between intrinsically disordered transactivation domains and the KIX domain.
Q46554672	Deciphering the role of the electrostatic interactions in the alpha-tropomyosin head-to-tail complex
Q87241136	Decoding the structural events in substrate-gating mechanism of eukaryotic prolyl oligopeptidase using normal mode analysis and molecular dynamics simulations
Q52421487	Deconvolution of the circular dichroism spectra of proteins: the circular dichroism spectra of the antiparallel beta-sheet in proteins
Q30420763	Decoupling of melting domains in immobilized ribonuclease A.
Q92749482	Decrypting protein surfaces by combining evolution, geometry, and molecular docking
Q27640178	Deep trefoil knot implicated in RNA binding found in an archaebacterial protein
Q92309343	Deep-learning contact-map guided protein structure prediction in CASP13
Q30425238	Defining a similarity threshold for a functional protein sequence pattern: the signal peptide cleavage site
Q51618751	Defining and characterizing protein surface using alpha shapes.
Q33248029	Defining the fold space of membrane proteins: the CAMPS database
Q47861597	Defining the limits of homology modeling in information-driven protein docking
Q47176446	Defining the protein complexome of translation termination factor eRF1: Identification of four novel eRF1-containing complexes that range from 20S to 57S in size.
Q30354491	Definition and classification of evaluation units for CASP10
Q45936967	Definition and classification of evaluation units for tertiary structure prediction in CASP12 facilitated through semi-automated metrics.
Q80538911	Definition of an electrostatic relay switch critical for the cAMP-dependent activation of protein kinase A as revealed by the D170A mutant of RIalpha
Q35655524	Deformability in the cleavage site of primary microRNA is not sensed by the double-stranded RNA binding domains in the microprocessor component DGCR8
Q30327742	Defrosting the frozen approximation: PROSPECTOR--a new approach to threading.
Q57120067	DelPhiPKa: Including salt in the calculations and enabling polar residues to titrate
Q30353658	Delaunay-based nonlocal interactions are sufficient and accurate in protein fold recognition.
Q28255720	Deletions and replacements of omega loops in yeast iso-1-cytochrome c
Q90516533	Delineation of a new structural motif involving NHN γ-turn
Q39398108	Delineation of key XRCC4/Ligase IV interfaces for targeted disruption of non-homologous end joining DNA repair
Q49265681	Denatured collapsed states in protein folding: example of apomyoglobin
Q30157773	Denatured state is critical in determining the properties of model proteins designed on different folds.
Q44927767	Density functional studies on herpes simplex virus type 1 thymidine kinase–substrate interactions: The role of Tyr-172 and Met-128 in thymine fixation
Q42189457	Density functional theory calculations on entire proteins for free energies of binding: application to a model polar binding site
Q83705648	Density-cluster NMA: A new protein decomposition technique for coarse-grained normal mode analysis
Q58847199	Dependence of folding dynamics and structural stability on the location of a hydrophobic pair in β-hairpins
Q30351652	Dependency between consecutive local conformations helps assemble protein structures from secondary structures using Go potential and greedy algorithm.
Q73393012	Derivation of protein-specific pair potentials based on weak sequence fragment similarity
Q85528303	Deriving how far structural information is transmitted through parallel homodimeric coiled-coils: a correlation analysis of helical staggers
Q30367959	Deriving protein dynamical properties from weighted protein contact number.
Q30375802	Describing protein structure: a general algorithm yielding complete helicoidal parameters and a unique overall axis.
Q30374836	Description and recognition of regular and distorted secondary structures in proteins using the automated protein structure analysis method.
Q79364295	Description of atomic burials in compact globular proteins by Fermi-Dirac probability distributions
Q46607611	Design and characterization of a multimeric DNA binding protein using Sac7d and GCN4 as templates
Q91188520	Design and characterization of novel dual Fc antibody with enhanced avidity for Fc receptors
Q30730691	Design and expression of soluble CTLA-4 variable domain as a scaffold for the display of functional polypeptides
Q44125145	Design and folding of dimeric proteins
Q43864568	Design and initial characterization of a circular permuted variant of the potent HIV-inactivating protein cyanovirin-N.
Q44739782	Design and synthesis of the pseudo-EF hand in calbindin D9K: effect of amino acid substitutions in the alpha-helical regions
Q92039518	Design of a basigin-mimicking inhibitor targeting the malaria invasion protein RH5
Q30977089	Design of a data model for developing laboratory information management and analysis systems for protein production
Q30408033	Design of a modified mouse protein with ligand binding properties of its human analog by molecular dynamics simulations: the case of C3 inhibition by compstatin
Q48218853	Design of anti-thyroid drugs: Binding studies and structure determination of the complex of lactoperoxidase with 2-mercaptoimidazole at 2.30 Å resolution
Q37797029	Design of biologically active, conformationally constrained GnRH antagonists
Q33218374	Design of combinatorial protein libraries of optimal size
Q57278499	Design of human granzyme B variants resistant to serpin B9
Q50762559	Design of improved protein inhibitors of HIV-1 cell entry: Optimization of electrostatic interactions at the binding interface.
Q72141147	Design of interchain disulfide bonds in the framework region of the Fv fragment of the monoclonal antibody B3
Q47588127	Design of multispecific protein sequences using probabilistic graphical modeling.
Q47810325	Design of proteins with hydrophobic and polar amino acids
Q57837586	Design principles for chlorophyll-binding sites in helical proteins
Q77142598	Design, construction, crystallization, and preliminary X-ray studies of a fine-tuning mutant (F133V) of module-substituted chimera hemoglobin
Q30978202	Design, docking, and evaluation of multiple libraries against multiple targets
Q78315769	Designability of protein structures: a lattice-model study using the Miyazawa-Jernigan matrix
Q44415585	Designing cooperativity into the designed protein Top7.
Q48254643	Designing dual inhibitors of Mdm2/MdmX: Unexpected coupling of water with gatekeeper Y100/99.
Q35783481	Designing proteins from the inside out.
Q54451017	Destabilization of transthyretin by pathogenic mutations in the DE loop
Q80538535	Detailed conformational dynamics of juxtamembrane region and activation loop in c-Kit kinase activation process
Q46991263	Detailed microscopic study of the full zipA:FtsZ interface.
Q52012567	Detecting distant homologs using phylogenetic tree-based HMMs
Q35803616	Detecting local ligand‐binding site similarity in nonhomologous proteins by surface patch comparison
Q30365803	Detecting local residue environment similarity for recognizing near-native structure models.
Q51990733	Detecting local structural similarity in proteins by maximizing number of equivalent residues
Q87661778	Detecting protein atom correlations using correlation of probability of recurrence
Q44754837	Detecting selection for negative design in proteins through an improved model of the misfolded state
Q36152480	Detecting the native ligand orientation by interfacial rigidity: SiteInterlock
Q84417770	Detection and refinement of encounter complexes for protein-protein docking: taking account of macromolecular crowding
Q80113373	Detection of a hidden folding intermediate in the focal adhesion target domain: Implications for its function and folding
Q73379992	Detection of breaking points in helices linking separate domains
Q52465662	Detection of common three-dimensional substructures in proteins
Q47285412	Detection of functional modules from protein interaction networks.
Q48405901	Detection of gene duplication signals of Ig folds from their amino acid sequences
Q52614830	Detection of human somatic cell structural gene mutations by two-dimensional electrophoresis
Q67538812	Detection of local structures in reduced unfolded bovine pancreatic trypsin inhibitor
Q51773359	Detection of multiscale pockets on protein surfaces using mathematical morphology.
Q30995797	Detection of native-like models for amino acid sequences of unknown three-dimensional structure in a data base of known protein conformations
Q31956710	Detection of non-covalent interaction of single and double stranded DNA with peptides by MALDI-TOF.
Q54464027	Detection of operons.
Q42925767	Detection of peptide-binding sites on protein surfaces: the first step toward the modeling and targeting of peptide-mediated interactions
Q38302586	Detection of pockets on protein surfaces using small and large probe spheres to find putative ligand binding sites.
Q51356483	Detection of protein complexes using a protein ranking algorithm
Q51052614	Detection of structural changes in a cofactor binding protein by using a wheat germ cell-free protein synthesis system coupled with unnatural amino acid probing
Q45099918	Determinants of cysteine pKa values in creatine kinase and alpha1-antitrypsin
Q42665668	Determinants of protein stability and folding: comparative analysis of beta-lactoglobulins and liver basic fatty acid binding protein
Q30151151	Determination of binding affinity upon mutation for type I dockerin-cohesin complexes from Clostridium thermocellum and Clostridium cellulolyticum using deep sequencing
Q51939475	Determination of dihedral Psi angles in large proteins by combining NH(N)/C(alpha)H(alpha) dipole/dipole cross-correlation and chemical shifts
Q52327747	Determination of the conformation of folding initiation sites in proteins by computer simulation
Q83167336	Determination of the dipole moments of RNAse SA wild type and a basic mutant
Q92927072	Determination of the structural ensemble of the molten globule state of a protein by computer simulations
Q36457536	Determination of three-dimensional protein structures from nuclear magnetic resonance data using fragments of known structures
Q30371560	Determining and visualizing flexibility in protein structures.
Q34188709	Determining macromolecular assembly structures by molecular docking and fitting into an electron density map
Q27670984	Determining the molecular mechanism of inactivation by chemical modification of triosephosphate isomerase from the human parasite Giardia lamblia: a study for antiparasitic drug design
Q46770756	Deuterium oxide promotes assembly and bundling of FtsZ protofilaments
Q35561768	Developing hybrid approaches to predict pKavalues of ionizable groups
Q30361367	Development and benchmarking of TASSER(iter) for the iterative improvement of protein structure predictions.
Q31086785	Development and large scale benchmark testing of the PROSPECTOR_3 threading algorithm
Q51970518	Development and testing of an automated approach to protein docking
Q47299338	Development of METAL-ACTIVE SITE and ZINCCLUSTER tool to predictactive site pockets
Q36145651	Development of a motif-based topology-independent structure comparison method to identify evolutionarily related folds
Q42109476	Development of a new physics‐based internal coordinate mechanics force field and its application to protein loop modeling
Q33314112	Development of new laccases by directed evolution: functional and computational analyses
Q40295007	Development, validation, and application of adapted PEOE charges to estimate pKa values of functional groups in protein-ligand complexes
Q40270287	Dewetting transitions in protein cavities
Q52259049	Dichroic statistical model for prediction and analysis of peptide helicity
Q30323904	Dictionary building via unsupervised hierarchical motif discovery in the sequence space of natural proteins.
Q30431465	Dictionary of recurrent domains in protein structures
Q68085494	Differences in crystal properties and ligand affinities of an antifluorescyl Fab (4-4-20) in two solvent systems
Q60214193	Differences in the effects of TFE on the folding pathways of human stefins A and B
Q28822370	Different combinations of atomic interactions predict protein-small molecule and protein-DNA/RNA affinities with similar accuracy
Q27685402	Different contribution of conserved amino acids to the global properties of triosephosphate isomerases
Q30397736	Different dynamics and pathway of disulfide bonds reduction of two human defensins, a molecular dynamics simulation study
Q46619319	Different methylation characteristics of protein arginine methyltransferase 1 and 3 toward the Ewing Sarcoma protein and a peptide
Q47867012	Different propensity to form amyloid fibrils by two homologous proteins-Human stefins A and B: searching for an explanation.
Q58045315	Different secondary structure elements as scaffolds for protein folding transition states of two homologous four-helix bundles
Q30573849	Different sequence patterns in signal peptides from mycoplasmas, other gram-positive bacteria, and Escherichia coli: a multivariate data analysis
Q48591816	Differentiable, multi-dimensional, knowledge-based energy terms for torsion angle probabilities and propensities
Q50593026	Differential dynamics of RAS isoforms in GDP- and GTP-bound states
Q43026130	Differential effects of Phe19 and Phe20 on fibril formation by amyloidogenic peptide A beta 16-22 (Ac-KLVFFAE-NH2).
Q43728441	Differential effects of isomeric incorporation of fluorophenylalanines into PvuII endonuclease
Q81388887	Differential native state ruggedness of the two Ca2+-binding domains in a Ca2+ sensor protein
Q73228382	Differential pathways in oxy and deoxy HbC aggregation/crystallization
Q83199912	Differential role of calmodulin and calcium ions in the stabilization of the catalytic domain of adenyl cyclase CyaA from Bordetella pertussis
Q78675911	Differential scanning calorimetric, circular dichroism, and Fourier transform infrared spectroscopic characterization of the thermal unfolding of xylanase A from Streptomyces lividans
Q46814791	Differentiation between two-state and multi-state folding proteins based on sequence
Q33232127	Differentiation-dependent expression of hypothetical proteins in the neuroblastoma cell line N1E-115.
Q68052814	Diffusion-collision model for the folding kinetics of myoglobin
Q56997925	Diffusion-collision of foldons elucidates the kinetic effects of point mutations and suggests control strategies of the folding process of helical proteins
Q98228003	Dihydrolipoamide dehydrogenase moonlighting activity as a DNA chelating agent
Q96584727	Dimerization of Aβ40 inside dipalmitoylphosphatidylcholine bilayer and its effect on bilayer integrity: Atomistic simulation at three temperatures
Q57970601	Dimerization of protein G B1 domain at low pH: A conformational switch caused by loss of a single hydrogen bond
Q42654611	Dipeptide frequency/bias analysis identifies conserved sites of nonrandomness shared by cysteine-rich motifs
Q74246359	Dipole lattice membrane model for protein calculations
Q51646349	Direct computation of long time processes in peptides and proteins: reaction path study of the coil-to-helix transition in polyalanine
Q51139925	Direct correlation between proteins' folding rates and their amino acid compositions: an ab initio folding rate prediction
Q79298609	Direct folding simulation of alpha-helices and beta-hairpins based on a single all-atom force field with an implicit solvation model
Q46764625	Direct insight into insulin aggregation by 2D NMR complemented by PFGSE NMR.
Q43015686	Direct measure of functional importance visualized atom-by-atom for photoactive yellow protein: application to photoisomerization reaction
Q46906261	Direct observation of an altered quaternary-structure transition in a mutant aspartate transcarbamoylase
Q30363288	Direct prediction of profiles of sequences compatible with a protein structure by neural networks with fragment-based local and energy-based nonlocal profiles
Q51304377	Directed evolution of the epidermal growth factor receptor extracellular domain for expression in yeast
Q42232452	Discerning intersecting fusion-activation pathways in the Nipah virus using machine learning
Q40359179	Discovery of Rab1 binding sites using an ensemble of clustering methods
Q35172930	Discovery of binding proteins for a protein target using protein-protein docking-based virtual screening
Q52224068	Discovery of local packing motifs in protein structures
Q39043145	Discovery of multiple interacting partners of gankyrin, a proteasomal chaperone and an oncoprotein--evidence for a common hot spot site at the interface and its functional relevance.
Q91821912	Discovery of receptor-ligand interfaces in the immunoglobulin superfamily
Q37343613	Discovery of sarcosine dimethylglycine methyltransferase from Galdieria sulphuraria.
Q47620467	Discriminating between homodimeric and monomeric proteins in the crystalline state
Q52236828	Discrimination between native and intentionally misfolded conformations of proteins: ES/IS, a new method for calculating conformational free energy that uses both dynamics simulations with an explicit solvent and an implicit solvent continuum model
Q43023250	Discrimination of mesophilic and thermophilic proteins using machine learning algorithms
Q31153497	Discrimination of native loop conformations in membrane proteins: decoy library design and evaluation of effective energy scoring functions.
Q58489192	Discrimination of near-native protein structures from misfolded models by empirical free energy functions
Q30327412	Discrimination of near-native protein structures from misfolded models by empirical free energy functions.
Q33662936	Discrimination of near-native structures in protein-protein docking by testing the stability of local minima
Q45966107	Discrimination of outer membrane proteins using machine learning algorithms.
Q44855355	Discrimination of single amino acid mutations of the p53 protein by means of deterministic singularities of recurrence quantification analysis
Q74721860	Discriminative ability with respect to amino acid types: assessing the performance of knowledge-based potentials without threading
Q30368864	Discriminative learning for protein conformation sampling.
Q34508241	Disorder and order in unfolded and disordered peptides and proteins: a view derived from tripeptide conformational analysis. I. Tripeptides with long and predominantly hydrophobic side chains
Q43658168	Disorder and order in unfolded and disordered peptides and proteins: a view derived from tripeptide conformational analysis. II. Tripeptides with short side chains populating asx and β-type like turn conformations
Q58429273	Disorder guides domain rearrangement in elongation factor Tu
Q34064614	Disposition of amphiphilic helices in heteropolar environments
Q57951719	Dissecting contact potentials for proteins: Relative contributions of individual amino acids
Q77926233	Dissecting protein-protein recognition sites
Q44632584	Dissecting subunit interfaces in homodimeric proteins
Q52698759	Dissecting the molecular mechanism of drosophila odorant receptors through activity modeling and comparative analysis
Q30385799	Dissecting the roles of local packing density and longer-range effects in protein sequence evolution
Q47974543	Dissecting α-helices: Position-specific analysis of α-helices in globular proteins
Q60162161	Dissection of multi-protein complexes using mass spectrometry: Subunit interactions in transthyretin and retinol-binding protein complexes
Q31956726	Dissection of multi-protein complexes using mass spectrometry: subunit interactions in transthyretin and retinol-binding protein complexes
Q46403154	Dissection of the GTPase mechanism of Ras protein by MD analysis of Ras mutants
Q42935474	Dissection of the conformational cycle of the multidrug/lipidA ABC exporter MsbA.
Q37732202	Dissection of the critical binding determinants of cellular retinoic acid binding protein II by mutagenesis and fluorescence binding assay
Q81787002	Dissection, residue conservation, and structural classification of protein-DNA interfaces
Q91325492	Dissociation mechanism of GDP from Cdc42 via DOCK9 revealed by molecular dynamics simulations
Q44252305	Distal heme pocket regulation of ligand binding and stability in soybean leghemoglobin
Q82354920	Distal mutation modulates the heme sliding in mouse neuroglobin investigated by molecular dynamics simulation
Q30364498	Distance dependent centroid to centroid force fields using high resolution decoys.
Q51690029	Distance-dependent classification of amino acids by information theory
Q74177419	Distance-dependent, pair potential for protein folding: results from linear optimization
Q51454003	Distance‐dependent atomic knowledge‐based force in protein fold recognition
Q33310035	Distant homology detection using a LEngth and STructure-based sequence Alignment Tool (LESTAT).
Q30429638	Distant homology recognition using structural classification of proteins
Q55122146	Distant homology recognition using structural classification of proteins
Q43017790	Distinct character in hydrophobicity of amino acid compositions of mitochondrial proteins
Q38789349	Distinct dynamics and interaction patterns in H- and K-Ras oncogenic P-loop mutants
Q45349661	Distinct interfacial biclique patterns between ssDNA-binding proteins and those with dsDNAs
Q45115569	Distinct phases of free α-synuclein--a Monte Carlo study
Q42694873	Distinct second extracellular loop structures of the brain cannabinoid CB(1) receptor: implication in ligand binding and receptor function
Q96339144	Distinctive Communication Networks in Inactive States of β2 -Adrenergic Receptor: Mutual Information and Entropy Transfer Analysis
Q92513880	Distinctive ligand-binding specificities of tandem PA14 biomass-sensory elements from Clostridium thermocellum and Clostridium clariflavum
Q47715113	Distinguish protein decoys by using a scoring function based on a new AMBER force field, short molecular dynamics simulations, and the generalized born solvent model
Q38438050	Distinguishing between biochemical and cellular function: Are there peptide signatures for cellular function of proteins?
Q52033392	Distinguishing foldable proteins from nonfolders: when and how do they differ?
Q57134711	Distinguishing native conformations of proteins from decoys with an effective free energy estimator based on the OPLS all-atom force field and the Surface Generalized Born solvent model
Q45946546	Distinguishing two groups of flavin reductases by analyzing the protonation state of an active site carboxylic acid
Q70140031	Distribution and complementarity of hydropathy in multisubunit proteins
Q36747528	Distribution function implied dynamics versus residence times and correlations: solvation shells of myoglobin
Q74460972	Distribution of Indel lengths
Q41443860	Distribution of accessible surfaces of amino acids in globular proteins
Q30330311	Distributions of beta sheets in proteins with application to structure prediction.
Q41736278	Disulfide bond plasticity in epidermal growth factor
Q30156089	Disulfide bond tethering of extracellular loops does not affect the closure of OmpF porin at acidic pH.
Q38113990	Disulfide bonds in amyloidogenesis diseases related proteins
Q90297462	Disulfide bridge formation influences ligand recognition by the ATAD2 bromodomain
Q43235819	Disulfide conformation and design at helix N-termini
Q30353891	Disulfide connectivity prediction with 70% accuracy using two-level models.
Q28662264	Diterpene cyclases and the nature of the isoprene fold
Q81471426	Divalent ion-binding properties of the two avian beta-parvalbumins
Q46263456	Diversity in peptide recognition by the SH2 domain of SH2B1.
Q33790634	Diversity of conformational states and changes within the EF-hand protein superfamily
Q51903856	Do collagenases unwind triple-helical collagen before peptide bond hydrolysis? Reinterpreting experimental observations with mathematical models
Q34049826	Do crystal structures obviate the need for theoretical models of GPCRs for structure-based virtual screening?
Q57851365	Do more complex organisms have a greater proportion of membrane proteins in their genomes?
Q29038132	DockRank: Ranking docked conformations using partner-specific sequence homology-based protein interface prediction
Q30432061	DockTrina: docking triangular protein trimers.
Q42080846	Docking analysis of transient complexes: interaction of ferredoxin-NADP+ reductase with ferredoxin and flavodoxin
Q31031991	Docking and free energy simulations to predict conformational domains involved in hCG-LH receptor interactions using recombinant antibodies
Q30008752	Docking and molecular dynamics simulations of the Fyn-SH3 domain with free and phospholipid bilayer-associated 18.5-kDa myelin basic protein (MBP)-Insights into a noncanonical and fuzzy interaction
Q28252297	Docking and scoring protein complexes: CAPRI 3rd Edition
Q47584586	Docking and scoring protein interactions: CAPRI 2009
Q33360334	Docking and scoring with alternative side-chain conformations
Q33660432	Docking by structural similarity at protein-protein interfaces
Q71671442	Docking enzyme-inhibitor complexes using a preference-based free-energy surface
Q28258497	Docking essential dynamics eigenstructures
Q43512278	Docking molecules by families to increase the diversity of hits in database screens: computational strategy and experimental evaluation
Q42164220	Docking multiple conformations of a flexible ligand into a protein binding site using NMR restraints
Q43946825	Docking of a human rhinovirus neutralizing antibody onto the viral capsid
Q52216410	Docking of flexible ligands to flexible receptors in solution by molecular dynamics simulation
Q31062350	Docking of human interleukin-15 to its specific receptor alpha chain: correlation between molecular modeling and mutagenesis experimental data
Q82693119	Docking of insulin to a structurally equilibrated insulin receptor ectodomain
Q44195803	Docking of non-nucleoside inhibitors: neotripterifordin and its derivatives to HIV-1 reverse transcriptase
Q51906606	Docking of protein molecular surfaces with evolutionary trace analysis
Q51970527	Docking prediction using biological information, ZDOCK sampling technique, and clustering guided by the DFIRE statistical energy function
Q91349200	Docking proteins and peptides under evolutionary constraints in Critical Assessment of PRediction of Interactions rounds 38 to 45
Q33196433	Docking studies and model development of tea polyphenol proteasome inhibitors: applications to rational drug design
Q51970501	Docking to single-domain and multiple-domain proteins: old and new challenges
Q52042875	Docking unbound proteins using shape complementarity, desolvation, and electrostatics
Q40174451	Docking with PIPER and refinement with SDU in rounds 6-11 of CAPRI.
Q33297369	Docking without docking: ISEARCH--prediction of interactions using known interfaces
Q38312001	Docking, scoring, and affinity prediction in CAPRI.
Q90996706	Dodecameric structure of a small heat shock protein from Mycobacterium marinum M
Q92439107	Does inclusion of residue-residue contact information boost protein threading?
Q51966376	Does secondary structure determine tertiary structure in proteins?
Q81635423	Does structural and chemical divergence play a role in precluding undesirable protein interactions?
Q57599858	Does tetracycline bind helix 2 of prion? An integrated spectroscopical and computational study of the interaction between the antibiotic and α helix 2 human prion protein fragments
Q57931515	Domain definition and target classification for CASP6
Q56879564	Domain definition and target classification for CASP7
Q43726275	Domain flexibility in aspartic proteinases
Q46850356	Domain interactions direct misfolding and amyloid formation of yeast phosphoglycerate kinase.
Q32063337	Domain motions in bacteriophage T4 lysozyme: a comparison between molecular dynamics and crystallographic data.
Q46194103	Domain motions of hyaluronan lyase underlying processive hyaluronan translocation.
Q30374966	Domain position prediction based on sequence information by using fuzzy mean operator.
Q125822463	Domain shuffling of a highly mutable ligand‐binding fold drives adhesin generation across the bacterial kingdom
Q34342990	Domain swapping of CD4 upon dimerization
Q43676309	Don Caspar, TMV, and protein–protein interactions
Q52291822	Dopamine transporter comparative molecular modeling and binding site prediction using the LeuT(Aa) leucine transporter as a template
Q51433130	Double phosphorylation-induced structural changes in the signal-receiving domain of IκBα in complex with NF-κB.
Q39702497	Dowser++, a new method of hydrating protein structures
Q54013266	Dramatic differences in the motions of the mouth of open and closed cytochrome P450BM-3 by molecular dynamics simulations
Q92737749	Driven to near-experimental accuracy by refinement via molecular dynamics simulations
Q42617629	Drug block of the hERG potassium channel: insight from modeling.
Q79402267	Drug design for the third world: a conference report
Q39856385	Dry molten globule intermediates and the mechanism of protein unfolding
Q53355939	Dual effects of familial Alzheimer's disease mutations (D7H, D7N, and H6R) on amyloid β peptide: correlation dynamics and zinc binding
Q46714089	Dual-affinity avidin molecules.
Q51766267	DynaDock: A new molecular dynamics-based algorithm for protein-peptide docking including receptor flexibility
Q51641989	Dynamic and structural analysis of isotropically distributed molecular ensembles
Q96233399	Dynamic aspects of pressure and temperature-stabilized intermediates of outer surface protein A
Q83413198	Dynamic communication between androgen and coactivator: mutually induced conformational perturbations in androgen receptor ligand-binding domain
Q83358893	Dynamic control of allosteric antagonism of leukocyte function antigen-1 and intercellular adhesion molecule-1 interaction
Q51940497	Dynamic domain threading
Q78675897	Dynamic effects of mutations within two loops of cytochrome c551 from Pseudomonas aeruginosa
Q83782525	Dynamic flaps in HIV‐1 protease adopt unique ordering at different stages in the catalytic cycle
Q44321993	Dynamic fluorescence studies of beta-glycosidase mutants from Sulfolobus solfataricus: effects of single mutations on protein thermostability.
Q52077719	Dynamic ligand design and combinatorial optimization: designing inhibitors to endothiapepsin
Q72061281	Dynamic properties of some beta-chain mutant hemoglobins
Q50909668	Dynamic property is a key determinant for protein-protein interactions
Q70980737	Dynamic structure of human serum transferrin from transient electric birefringence experiments
Q77142633	Dynamic structure of subtilisin-eglin c complex studied by normal mode analysis
Q22061744	Dynamic α-helices: Conformations that do not conform
Q79737558	Dynamical behavior of the vascular endothelial growth factor: biological implications
Q91294630	Dynamical comparison between myoglobin and hemoglobin
Q47865702	Dynamical differences of hemoglobin and the ionotropic glutamate receptor in different states revealed by a new dynamics alignment method.
Q56934603	Dynamical properties of fasciculin-2
Q41685635	Dynamical properties of fasciculin-2.
Q51438313	Dynamics alignment: comparison of protein dynamics in the SCOP database
Q50753745	Dynamics and allostery of the ionotropic glutamate receptors and the ligand binding domain
Q79223162	Dynamics and assembly of the cytolethal distending toxin
Q44898271	Dynamics and energetics of water permeation through the aquaporin channel
Q64032840	Dynamics and energetics of water permeation through the aquaporin channel
Q51799173	Dynamics and thermodynamic properties of CXCL7 chemokine.
Q27734335	Dynamics of Fusarium solani cutinase investigated through structural comparison among different crystal forms of its variants
Q42617075	Dynamics of beta3 integrin I-like and hybrid domains: insight from simulations on the mechanism of transition between open and closed forms.
Q48091281	Dynamics of bridge helix bending in RNA polymerase II.
Q58847877	Dynamics of group II chaperonin and prefoldin probed by 13C NMR spectroscopy
Q80424010	Dynamics of heteropentameric nicotinic acetylcholine receptor: implications of the gating mechanism
Q73422367	Dynamics of internal water in fatty acid binding protein: computer simulations and comparison with experiments
Q47620838	Dynamics of proteins predicted by molecular dynamics simulations and analytical approaches: application to alpha-amylase inhibitor
Q48058556	Dynamics of the protein structure of T169S pyranose 2-oxidase in solution: Molecular dynamics simulation
Q37249169	Dynamics of the trimeric AcrB transporter protein inferred from a B-factor analysis of the crystal structure
Q86212715	Dynamics on human Toll-like receptor 4 complexation to MD-2: the coreceptor stabilizing function
Q27681811	E2-binding surface on Uba3 β-grasp domain undergoes a conformational transition
Q51919234	EADock: docking of small molecules into protein active sites with a multiobjective evolutionary optimization.
Q34113376	EVA: large-scale analysis of secondary structure prediction
Q44431730	Early days of protein hydrogen exchange: 1954–1972
Q80962914	Early events in protein aggregation: molecular flexibility and hydrophobicity/charge interaction in amyloid peptides as studied by molecular dynamics simulations
Q52206952	Early events in the folding of an amphipathic peptide: A multinanosecond molecular dynamics study
Q81430221	Early stages of beta2-microglobulin aggregation and the inhibiting action of alphaB-crystallin
Q52237300	Easy method to predict solvent accessibility from multiple protein sequence alignments
Q57385264	Edge-count probabilities for the identification of local protein communities and their organization
Q73379942	Editorial on molecular dynamics simulations
Q114234886	Editorial: Special issue Transporter and Channel
Q27654075	Effect of D to E mutation of the RGD motif in rhodostomin on its activity, structure, and dynamics: importance of the interactions between the D residue and integrin
Q74631434	Effect of G40R mutation on the binding of human SRY protein to DNA: a molecular dynamics view
Q81081492	Effect of T-R conformational change on sickle-cell hemoglobin interactions and aggregation
Q30352687	Effect of a mutation on the structure and dynamics of an alpha-helical antifreeze protein in water and ice.
Q28217665	Effect of acidic phospholipids on the structural properties of recombinant cytosolic human glyoxalase II
Q30322344	Effect of alphabet size and foldability requirements on protein structure designability.
Q38290271	Effect of altered glycosylation on the structure of the I-like domain of beta1 integrin: a molecular dynamics study
Q74452352	Effect of amino acid substitutions at the subunit interface on the stability and aggregation properties of a dimeric protein: role of Arg 178 and Arg 218 at the Dimer interface of thymidylate synthase
Q50647078	Effect of an amyloidogenic sequence attached to yellow fluorescent protein
Q46814803	Effect of bivalent cations on the interaction of transketolase with its donor substrate
Q70628260	Effect of end group blockage on the properties of a class A amphipathic helical peptide
Q42162687	Effect of ethanol on folding of hen egg-white lysozyme under acidic condition
Q40336901	Effect of flanking residues on the conformational sampling of the internal fusion peptide from Ebola virus
Q34336924	Effect of glycosylation on the structure of Erythrina corallodendron lectin.
Q91966009	Effect of heterochiral inversions on the structure of a β-hairpin peptide
Q92822826	Effect of hydrophobic and hydrogen bonding interactions on the potency of ß-alanine analogs of G-protein coupled glucagon receptor inhibitors
Q40692587	Effect of intrinsic and extrinsic factors on the simulated D-band length of type I collagen.
Q48467606	Effect of linker segments on the stability of epithelial cadherin Domain 2.
Q81202526	Effect of lipid composition on buforin II structure and membrane entry
Q43144227	Effect of mixed macromolecular crowding agents on protein folding
Q43030638	Effect of naturally occurring active site mutations on hepatitis C virus NS3 protease specificity
Q47629351	Effect of nucleotide substrate binding on the pKa of catalytic residues in barnase
Q34501365	Effect of oxidatively damaged DNA on the active site preorganization during nucleotide incorporation in a high fidelity polymerase from Bacillus stearothermophilus.
Q46987563	Effect of pH on the structure and stability of Bacillus circulans ssp. alkalophilus phosphoserine aminotransferase: thermodynamic and crystallographic studies.
Q67562114	Effect of polyethylene glycol-400 at low concentrations on long-term growth of muscle phosphoglucomutase crystals from concentrated salt solutions
Q45733316	Effect of pressure on helix-coil transition of an alanine-based peptide: an FTIR study
Q45094177	Effect of protein conformation on rate of deamidation: ribonuclease A.
Q90267288	Effect of site-directed point mutations on protein misfolding: A simulation study
Q67703767	Effect of urey-bradley-shimanouchi force field on the harmonic dynamics of proteins
Q30395993	Effect of using suboptimal alignments in template-based protein structure prediction
Q42351313	Effective approach for calculations of absolute stability of proteins using focused dielectric constants
Q30369789	Effective connectivity profile: a structural representation that evidences the relationship between protein structures and sequences.
Q43410518	Effective discrimination between biologically relevant contacts and crystal packing contacts using new determinants
Q44496100	Effective energy function for proteins in lipid membranes
Q28142746	Effective energy function for proteins in solution
Q30353351	Effective handling of induced-fit motion in flexible docking.
Q81191021	Effective interactions between chaotropic agents and proteins
Q38985037	Effective protein model structure refinement by loop modeling and overall relaxation
Q51727992	Effective scoring function for protein sequence design
Q27690734	Effectiveness and limitations of local structural entropy optimization in the thermal stabilization of mesophilic and thermophilic adenylate kinases
Q103007699	Effects of Amino Acid Modifications on the Permeability of the Pentameric Sarcolipin Channel
Q91895665	Effects of PI(4,5)P2 concentration on the F-BAR domain membrane binding as revealed by coarse-grained simulations
Q44125147	Effects of a helix substitution on the folding mechanism of bovine alpha-lactalbumin.
Q53754105	Effects of acid exposure on the conformation, stability, and aggregation of monoclonal antibodies
Q47298784	Effects of amino acid composition, finite size of proteins, and sparse statistics on distance-dependent statistical pair potentials
Q70830940	Effects of cavity-creating mutations on conformational stability and structure of the dimeric 4-alpha-helical protein ROP: thermal unfolding studies
Q44868395	Effects of chain length on the aggregation of model polyglutamine peptides: molecular dynamics simulations
Q67562112	Effects of changing the interaction between subdomains on the thermostability of Bacillus neutral proteases
Q52206946	Effects of core-packing on the structure, function, and mechanics of a four-helix-bundle protein ROP.
Q57276506	Effects of eglin-c binding to thermitase: Three-dimensional structure comparison of native thermitase and thermitase eglin-c complexes
Q30351693	Effects of environment on the structure of Pyrococcus furiosus rubredoxin: a molecular dynamics study.
Q30368087	Effects of external interactions on protein sequence-structure relations of beta-trefoil fold.
Q47299318	Effects of force fields on the conformational and dynamic properties of amyloid β(1-40) dimer explored by replica exchange molecular dynamics simulations
Q46899106	Effects of glycerol on the compaction and stability of the wild type and mutated rabbit muscle creatine kinase
Q38333301	Effects of glycosylation on heparin binding and antithrombin activation by heparin
Q80865702	Effects of ligand binding on the dynamics of rice nonspecific lipid transfer protein 1: a model from molecular simulations
Q50952462	Effects of ligand binding upon flexibility of proteins.
Q35933586	Effects of mutations in tyrosine hydroxylase associated with progressive dystonia on the activity and stability of the protein.
Q32167485	Effects of organic solvents on protein structures: Observation of a structured helical core in hen egg-white lysozyme in aqueous dimethylsulfoxide
Q41652279	Effects of pH and high ionic strength on the adsorption and activity of native and mutated cellobiohydrolase I from Trichoderma reesei
Q52618590	Effects of point mutations in pVHL on the binding of HIF-1α.
Q30414469	Effects of point mutations on protein structure are nonexponentially distributed.
Q27682066	Effects of protein engineering and rational mutagenesis on crystal lattice of single chain antibody fragments
Q42680896	Effects of protonation state of Asp181 and position of active site water molecules on the conformation of PTP1B
Q58043781	Effects of somatic mutations on CDR loop flexibility during affinity maturation
Q52237297	Effects of the T→R transition on the electrostatic properties ofE. coli aspartate transcarbamylase
Q85076899	Effects of the Val211Gly substitution on molecular dynamics of the CMY‐2 cephalosporinase: Implications on hydrolysis of expanded‐spectrum cephalosporins
Q46668377	Effects of the stabilization of the molten globule state on the folding mechanism of alpha-lactalbumin: a study of a chimera of bovine and human alpha-lactalbumin
Q52133669	Efficacy and selectivity in flexible database docking
Q45039422	Efficiency of a second-generation HIV-1 protease inhibitor studied by molecular dynamics and absolute binding free energy calculations.
Q78627277	Efficient RMSD measures for the comparison of two molecular ensembles. Root-mean-square deviation
Q51905248	Efficient comprehensive scoring of docked protein complexes using probabilistic support vector machines
Q30620916	Efficient electrostatic solvation model for protein-fragment docking
Q30380043	Efficient identification of near-native conformations in ab initio protein structure prediction using structural profiles.
Q44322005	Efficient identification of side-chain patterns using a multidimensional index tree
Q84266182	Efficient mapping of ligand migration channel networks in dynamic proteins
Q47236428	Efficient methods for filtering and ranking fragments for the prediction of structurally variable regions in proteins
Q56999374	Efficient minimization of angle-dependent potentials for polypeptides in internal coordinates
Q52920397	Efficient sampling in collective coordinate space
Q47653322	Elastic Surface Model For Beta-Barrels: Geometric, Computational, And Statistical Analysis.
Q46736038	Elastic network model‐based normal mode analysis reveals the conformational couplings in the tripartite AcrAB‐TolC multidrug efflux complex
Q54765737	Elastic network normal mode dynamics reveal the GPCR activation mechanism.
Q46141328	Electron redistribution on binding of a substrate to an enzyme: folate and dihydrofolate reductase
Q81319554	Electrospray ionization mass spectrometry of soybean lipoxygenases: N-terminal acetylation, chemical modification, and solution conformation
Q46815493	Electrostatic analysis of bacterial expansins.
Q69825129	Electrostatic calculations and model-building suggest that DNA bound to CAP is sharply bent
Q40305520	Electrostatic contribution to the binding stability of protein-protein complexes.
Q80867942	Electrostatic contribution to the thermodynamic and kinetic stability of the homotrimeric coiled coil Lpp-56: A computational study
Q46345768	Electrostatic contributions to protein–protein binding affinities: Application to Rap/Raf interaction
Q57138618	Electrostatic effects in a large enzyme complex: subunit interactions and electrostatic potential field of the icosahedral beta 60 capsid of heavy riboflavin synthase
Q45145991	Electrostatic fields at the active site of ribulose-1,5-bisphosphate carboxylase
Q90919807	Electrostatic interactions determine entrance/release order of substrates in the catalytic cycle of adenylate kinase
Q69518563	Electrostatic interactions in the assembly of Escherichia coli aspartate transcarbamylase
Q46870565	Electrostatic interactions of peptides flanking the tyrosine kinase domain in the epidermal growth factor receptor provides a model for intracellular dimerization and autophosphorylation.
Q39317330	Electrostatic interactions play an essential role in the binding of oleic acid with α‐lactalbumin in the HAMLET‐like complex: A study using charge‐specific chemical modifications
Q51549409	Electrostatic pKa computations in proteins: Role of internal cavities
Q46773035	Electrostatic potential at the retinal of three archaeal rhodopsins: implications for their different absorption spectra
Q71705238	Electrostatic properties deduced from refined structures of NADH-cytochrome b5 reductase and the other flavin-dependent reductases: pyridine nucleotide-binding and interaction with an electron-transfer partner
Q44496105	Electrostatic properties in the catalytic site of papain: A possible regulatory mechanism for the reactivity of the ion pair
Q57135485	Electrostatic properties of bovine beta-lactoglobulin
Q41780888	Electrostatic rate enhancement and transient complex of protein-protein association
Q39705849	Electrostatic repulsion between HIV-1 capsid proteins modulates hexamer plasticity and in vitro assembly
Q77924659	Electrostatic reversal of serine proteinase substrate specificity
Q30326371	Electrostatic strengths of salt bridges in thermophilic and mesophilic glutamate dehydrogenase monomers.
Q30418989	Electrostatics of cysteine residues in proteins: parameterization and validation of a simple model.
Q52077723	Electrostatics of mesophilic and psychrophilic trypsin isoenzymes: qualitative evaluation of electrostatic differences at the substrate binding site
Q52263620	Electrostatics of proteins: description in terms of two dielectric constants simultaneously
Q47625563	Electrostatics, allostery, and activity of the yeast chorismate mutase
Q46489549	Electrostatics-defying interaction between arginine termini as a thermodynamic driving force in protein-protein interaction
Q111199748	Elucidating important structural features for the binding affinity of spike - SARS-CoV-2 neutralizing antibody complexes
Q43676085	Elucidating protein secondary structures using alpha-carbon recurrence quantifications
Q27656422	Elucidating the exact role of engineered CRABPII residues for the formation of a retinal protonated Schiff base
Q52066466	Elucidating the structural mechanisms for biological activity of the chemokine family
Q45169306	Elucidation of information encoded in tryptophan 140 of staphylococcal nuclease
Q47195044	Elucidation of insulin assembly at acidic and neutral pH: Characterization of low molecular weight oligomers.
Q79210085	Elucidation of the disulfide-folding pathway of hirudin by a topology-based approach
Q40708038	Elucidation of the mode of substrate binding to hydroxynitrile lyase from Hevea brasiliensis.
Q72154714	Elusive affinities
Q53873970	Emergence of highly designable protein-backbone conformations in an off-lattice model
Q73864357	Empirical calculation of the relative free energies of peptide binding to the molecular chaperone DnaK
Q52335314	Empirical correlation for the replacement of Ala by Gly: importance of amino acid secondary intrinsic propensities
Q52340727	Empirical evaluation of the influence of side chains on the conformational entropy of the polypeptide backbone
Q46403139	Empirical lipid propensities of amino acid residues in multispan alpha helical membrane proteins
Q30352947	Empirical potential function for simplified protein models: combining contact and local sequence-structure descriptors.
Q30331170	Empirical relationships between protein structure and carboxyl pKa values in proteins.
Q31083650	Empirical solvation models can be used to differentiate native from near-native conformations of bovine pancreatic trypsin inhibitor
Q30852972	Empirical solvation models in the context of conformational energy searches: application to bovine pancreatic trypsin inhibitor
Q50104360	Empirical valence bond simulations of the hydride transfer step in the monoamine oxidase B catalyzed metabolism of dopamine
Q92952314	Enabling full-length evolutionary profiles based deep convolutional neural network for predicting DNA-binding proteins from sequence
Q44464209	Endogenous tryptophan residues of cAPK regulatory subunit type IIbeta reveal local variations in environments and dynamics
Q30195753	Energetic approach to the folding of α/β barrels
Q93171278	Energetic contributions of amino acid residues and its cross-talk (ECONTACT) to delineate ligand binding mechanism
Q36859545	Energetically unfavorable amide conformations for N6‐acetyllysine side chains in refined protein structures
Q81508069	Energetics and stability of transmembrane helix packing: a replica-exchange simulation with a knowledge-based membrane potential
Q53542878	Energetics of K+ permeability through Gramicidin A by forward-reverse steered molecular dynamics.
Q34074679	Energetics of calmodulin domain interactions with the calmodulin binding domain of CaMKII.
Q52427206	Energetics of charge-charge interactions in proteins
Q82451708	Energetics of charge–charge interactions between residues adjacent in sequence
Q81383313	Energetics of protein homodimerization: effects of water sequestering on the formation of beta-lactoglobulin dimer
Q45393738	Energetics of the loop-to-helix transition leading to the coiled-coil structure of influenza virus hemagglutinin HA2 subunits
Q82184337	Energetics of the native and non-native states of the glycophorin transmembrane helix dimer
Q73025531	Energetics of the specific binding interaction of the first three zinc fingers of the transcription factor TFIIIA with its cognate DNA sequence
Q30195936	Energetics of the structure and chain tilting of antiparallel beta-barrels in proteins
Q77669672	Energy landscape of a native protein: jumping-among-minima model
Q80947716	Energy landscape of a small peptide revealed by dihedral angle principal component analysis
Q53344184	Energy landscape theory for Alzheimer's amyloid beta-peptide fibril elongation
Q50923993	Energy minimization in low-frequency normal modes to efficiently allow for global flexibility during systematic protein-protein docking
Q30419952	Energy minimization method using automata network for sequence and side-chain conformation prediction from given backbone geometry.
Q90123830	Energy-based graph convolutional networks for scoring protein docking models
Q33447473	Engineered cystine knot peptides that bind alphavbeta3, alphavbeta5, and alpha5beta1 integrins with low-nanomolar affinity
Q60147785	Engineering a soluble parathyroid hormone GPCR mimetic
Q57077684	Engineering an Mg2 site to replace a structurally conserved arginine in the catalytic center of histidyl‐tRNA synthetase by computer experiments
Q77142657	Engineering an Mg2+ site to replace a structurally conserved arginine in the catalytic center of histidyl-tRNA synthetase by computer experiments
Q46020524	Engineering monomeric streptavidin and its ligands with infinite affinity in binding but reversibility in interaction.
Q33207176	Engineering of a polymeric bacterial protein as a scaffold for the multiple display of peptides.
Q74464024	Engineering of a stable mutant malic enzyme by introducing an extra ion-pair to the protein
Q41947472	Engineering proteins with enhanced mechanical stability by force-specific sequence motifs.
Q50890574	Engineering proteins with tunable thermodynamic and kinetic stabilities.
Q45948249	Engineering subtilisin BPN' for site-specific proteolysis.
Q96163609	Engineering the specificity of Streptococcus pyogenes sortase A by loop grafting
Q52082493	Enhanced conformational diversity search of CDR-H3 in antibodies: role of the first CDR-H3 residue
Q30373977	Enhanced protein fold recognition using a structural alphabet.
Q30350621	Enhanced sampling near the native conformation using statistical potentials for local side-chain and backbone interactions.
Q51101606	Enhanced sampling of peptide and protein conformations using replica exchange simulations with a peptide backbone biasing-potential
Q91163245	Enhanced sampling of protein conformational states for dynamic cross-docking within the protein-protein docking server SwarmDock
Q81134288	Enhanced thermal stability achieved without increased conformational rigidity at physiological temperatures: spatial propagation of differential flexibility in rubredoxin hybrids
Q27621917	Enhancement of catalytic efficiency of enzymes through exposure to anhydrous organic solvent at 70 degrees C. Three-dimensional structure of a treated serine proteinase at 2.2 A resolution
Q30329565	Enhancement of protein modeling by human intervention in applying the automatic programs 3D-JIGSAW and 3D-PSSM.
Q51531290	Enhancing systematic protein–protein docking methods using ray casting: Application to ATTRACT
Q95310337	Enhancing the promiscuity of a member of the Caspase protease family by rational design
Q52005574	Enriching the sequence substitution matrix by structural information
Q30357936	Ensemble docking of multiple protein structures: considering protein structural variations in molecular docking.
Q30010207	Ensemble modeling of protein disordered states: Experimental restraint contributions and validation
Q50688427	Ensemble models of proteins and protein domains based on distance distribution restraints
Q30351810	Ensemble-based signatures of energy propagation in proteins: a new view of an old phenomenon.
Q92585784	Ensembling multiple raw coevolutionary features with deep residual neural networks for contact-map prediction in CASP13
Q77435967	Enthalpy and heat capacity changes for the proton dissociation of various buffer components in 0.1 M potassium chloride
Q74449650	Entropic benefit of a cross-link in protein association
Q52068717	Entropy calculations on a reversibly folding peptide: changes in solute free energy cannot explain folding behavior
Q57204703	Entropy calculations on the molten globule state of a protein: Side-chain entropies of α-lactalbumin
Q58037819	Entropy capacity determines protein folding
Q52384808	Entropy in biological binding processes: estimation of translational entropy loss
Q30326388	Environment of tryptophan side chains in proteins.
Q27649989	Enzymatic characterization and crystal structure analysis of the D-alanine-D-alanine ligase from Helicobacter pylori
Q38302248	Enzymatic circularization of a malto-octaose linear chain studied by stochastic reaction path calculations on cyclodextrin glycosyltransferase
Q43530741	Enzyme classification by ligand binding
Q48007508	Enzyme family classification by support vector machines
Q73233198	Enzyme polarization of substrates of dihydrofolate reductase by different theoretical methods
Q27643332	Enzyme-substrate interactions revealed by the crystal structures of the archaeal Sulfolobus PTP-fold phosphatase and its phosphopeptide complexes
Q27648036	Epitope mapping and structural analysis of an anti-ErbB2 antibody A21: Molecular basis for tumor inhibitory mechanism
Q27703671	Epitope mapping and structural basis for the recognition of phosphorylated tau by the anti-tau antibody AT8
Q44195800	Equilibrium and kinetic folding of hen egg-white lysozyme under acidic conditions.
Q57752608	Equilibrium heat-induced denaturation of chitinase 40 from Streptomyces thermoviolaceus
Q30375057	Equilibrium transitions between side-chain conformations in leucine and isoleucine.
Q58375287	Erratum
Q95596616	Erratum
Q51940826	Error distribution derived NOE distance restraints.
Q91339294	Escapement mechanisms: Efficient free energy transduction by reciprocally-coupled gating
Q30428164	Escher: A new docking procedure applied to the reconstruction of protein tertiary structure
Q30961455	Escherichia coli adenylate kinase dynamics: comparison of elastic network model modes with mode-coupling (15)N-NMR relaxation data
Q77615139	Essential domain motions in barnase revealed by MD simulations
Q29616843	Essential dynamics of proteins
Q39226766	Essential dynamics of the cold denaturation: pressure and temperature effects in yeast frataxin
Q39135914	Essential dynamics sampling study of adenylate kinase: comparison to citrate synthase and implication for the hinge and shear mechanisms of domain motions
Q87726281	Essential function of the N-termini tails of the proteasome for the gating mechanism revealed by molecular dynamics simulations
Q47974629	Essential spaces defined by NMR structure ensembles and molecular dynamics simulation show significant overlap
Q78010858	Estimates of the loss of main-chain conformational entropy of different residues on protein folding
Q82354607	Estimating binding affinities by docking/scoring methods using variable protonation states
Q51610153	Estimating protein-ligand binding free energy: atomic solvation parameters for partition coefficient and solvation free energy calculation
Q51899745	Estimating quality of template-based protein models by alignment stability
Q64123395	Estimating the contribution of folding stability to nonspecific epistasis in protein evolution
Q39509181	Estimating the pKa values of basic and acidic side chains in ion channels using electrophysiological recordings: A robust approach to an elusive problem
Q33866133	Estimating the total number of protein folds
Q56032117	Estimating the total number of protein folds
Q52372237	Estimation of changes in side chain configurational entropy in binding and folding: general methods and application to helix formation
Q91550145	Estimation of model accuracy in CASP13
Q68697900	Estimation of uncertainties in X-ray refinement results by use of perturbed structures
Q30588359	Euclidean sections of protein conformation space and their implications in dimensionality reduction
Q52314555	Eukaryote Specific Folds: Part of the Whole.
Q30331647	Evaluating CASP4 predictions with physical energy functions.
Q48058205	Evaluating amber force fields using computed NMR chemical shifts.
Q81383307	Evaluating conformational changes in protein structures binding RNA
Q29547577	Evaluating protein structures determined by structural genomics consortia
Q50904735	Evaluating protein:protein complex formation using synchrotron radiation circular dichroism spectroscopy
Q30373259	Evaluating the absolute quality of a single protein model using structural features and support vector machines.
Q43196448	Evaluating the potency of HIV-1 protease drugs to combat resistance
Q31024907	Evaluating the quality of NMR structures by local density of protons
Q33855340	Evaluation and improvement of multiple sequence methods for protein secondary structure prediction.
Q30380203	Evaluation of CASP8 model quality predictions.
Q30429666	Evaluation of GRAMM low‐resolution docking methodology on the hemagglutinin‐antibody complex
Q28211559	Evaluation of a fast implicit solvent model for molecular dynamics simulations
Q33373402	Evaluation of an inverse molecular design algorithm in a model binding site
Q29617322	Evaluation of comparative protein modeling by MODELLER
Q30429627	Evaluation of comparative protein structure modeling by MODELLER‐3
Q42559661	Evaluation of conformational changes in diabetes-associated mutation in insulin a chain: a molecular dynamics study
Q30424408	Evaluation of current techniques for ab initio protein structure prediction
Q31031427	Evaluation of different biological data and computational classification methods for use in protein interaction prediction
Q57972076	Evaluation of disorder predictions in CASP5
Q29048164	Evaluation of disorder predictions in CASP9
Q27645460	Evaluation of docking programs for predicting binding of Golgi alpha-mannosidase II inhibitors: a comparison with crystallography
Q30351478	Evaluation of domain prediction in CASP6.
Q30382583	Evaluation of free modeling targets in CASP11 and ROLL.
Q68455955	Evaluation of homology modeling of HIV protease
Q30341344	Evaluation of local structure alphabets based on residue burial.
Q29048166	Evaluation of model quality predictions in CASP9
Q92309412	Evaluation of model refinement in CASP13
Q30352482	Evaluation of predictions in the CASP10 model refinement category.
Q52015248	Evaluation of protein docking predictions using Hex 3.1 in CAPRI rounds 1 and 2.
Q57014902	Evaluation of protein fold comparison servers
Q29048194	Evaluation of residue-residue contact prediction in CASP10
Q29048165	Evaluation of residue-residue contact predictions in CASP9
Q30322367	Evaluation of short-range interactions as secondary structure energies for protein fold and sequence recognition.
Q92585605	Evaluation of template-based modeling in CASP13
Q29048208	Evaluation of template-based models in CASP8 with standard measures
Q52015257	Evaluation of the 3D-Dock protein docking suite in rounds 1 and 2 of the CAPRI blind trial.
Q74252620	Evaluation of the CASP2 docking section
Q30822076	Evaluation of the FLEXX incremental construction algorithm for protein-ligand docking
Q54641591	Evaluation of the conformational free energies of loops in proteins.
Q37423462	Evaluation of the relative stability of liganded versus ligand-free protein conformations using Simplicial Neighborhood Analysis of Protein Packing (SNAPP) method
Q80252050	Evaluation of the substrate envelope hypothesis for inhibitors of HIV-1 protease
Q46357263	Evaluation of the template-based modeling in CASP12.
Q44464301	Evaluation of the third solvent clusters fitting procedure for the prediction of protein-protein interactions based on the results at the CAPRI blind docking study
Q71774359	Evaluation of threading specificity and accuracy
Q41642290	Evaluation of transmembrane helix predictions in 2014.
Q30531491	Event detection and sub‐state discovery from biomolecular simulations using higher‐order statistics: Application to enzyme adenylate kinase
Q30159592	Evidence for a novel domain of bacterial outer membrane ushers
Q46704187	Evidence for communality in the primary determinants of CYP74 catalysis and of structural similarities between CYP74 and classical mammalian P450 enzymes
Q84380451	Evidence for specific subunit distribution and interactions in the quaternary structure of alpha-crystallin
Q47974529	Evidence of new cadmium binding sites in recombinant horse L-chain ferritin by anomalous Fourier difference map calculation
Q36674676	Evidence of π‐stacking interactions in the self‐assembly of hIAPP22‐29
Q51537315	Evolution and similarity evaluation of protein structures in contact map space
Q30196048	Evolution of CuZn superoxide dismutase and the Greek key beta-barrel structural motif
Q30176869	Evolution of beta-amylase: patterns of variation and conservation in subfamily sequences in relation to parsimony mechanisms
Q47596509	Evolution of binding sites for zinc and calcium ions playing structural roles
Q61982092	Evolution of cnidarian trans-defensins: sequence, structure and exploration of chemical space
Q52251893	Evolution of model proteins on a foldability landscape
Q42614045	Evolution of prokaryotic subtilases: genome-wide analysis reveals novel subfamilies with different catalytic residues
Q112574716	Evolution of the SARS-CoV-2 proteome in three dimensions (3D) during the first 6 months of the COVID-19 pandemic
Q51973330	Evolution of the beta-propeller fold
Q83568740	Evolution of the isoelectric point of mammalian proteins as a consequence of indels and adaptive evolution
Q43994824	Evolutionary analysis of HIV-1 protease inhibitors: Methods for design of inhibitors that evade resistance
Q28204161	Evolutionary analysis reveals collective properties and specificity in the C-type lectin and lectin-like domain superfamily
Q85540701	Evolutionary and structural analyses of heterodimeric proteins composed of subunits with same fold
Q46883270	Evolutionary and structural feedback on selection of sequences for comparative analysis of proteins
Q51731627	Evolutionary conservation in multiple faces of protein interaction
Q46794959	Evolutionary conserved N-terminal region of human muscle fructose 1,6-bisphosphatase regulates its activity and the interaction with aldolase.
Q30159915	Evolutionary coupling of structural and functional sequence information in the intracellular lipid-binding protein family
Q90313520	Evolutionary couplings and sequence variation effect predict protein binding sites
Q42691196	Evolutionary identification of a subtype specific functional site in the ligand binding domain of steroid receptors
Q30414685	Evolutionary information hidden in a single protein structure
Q94566304	Evolutionary model of protein secondary structure capable of revealing new biological relationships
Q35928441	Evolutionary plasticity of protein families: coupling between sequence and structure variation
Q34371312	Evolutionary relationship between 5+5 and 7+7 inverted repeat folds within the amino acid-polyamine-organocation superfamily
Q96436206	Evolutionary relationships and sequence-structure determinants in human SARS coronavirus-2 spike proteins for host receptor recognition
Q44706742	Evolutionary trace analysis of scorpion toxins specific for K-channels
Q44631073	Examination of polypeptide substrate specificity for Escherichia coli ClpB.
Q47617870	Examination of possible structural constraints of MHC-binding peptides by assessment of their native structure within their source proteins.
Q47623070	Examination of shape complementarity in docking of unbound proteins
Q60651236	Examination of shape complementarity in docking ofUnbound proteins
Q53370116	Examination of the dynamic assembly equilibrium for E. coli ClpB.
Q41736269	Examining methods for calculations of binding free energies: LRA, LIE, PDLD-LRA, and PDLD/S-LRA calculations of ligands binding to an HIV protease
Q34139629	Examining the promiscuous phosphatase activity of Pseudomonas aeruginosa arylsulfatase: a comparison to analogous phosphatases.
Q46851137	Exhaustive Metropolis Monte Carlo sampling and analysis of polyalanine conformations adopted under the influence of hydrogen bonds
Q52206840	Exhaustive docking of molecular fragments with electrostatic solvation
Q46149002	Exhaustive mutagenesis in silico: multicoordinate free energy calculations on proteins and peptides
Q58488808	Expanded turn conformations: Characterization and sequence-structure correspondence in α-turns with implications in helix folding
Q44817538	Expanded turn conformations: characterization and sequence-structure correspondence in alpha-turns with implications in helix folding
Q46823172	Expanding GPCR homology model binding sites via a balloon potential: A molecular dynamics refinement approach
Q45775602	Expanding the frontiers of protein-protein modeling: from docking and scoring to binding affinity predictions and other challenges
Q74103023	Expanding the nitrogen regulatory protein superfamily: Homology detection at below random sequence identity
Q99627489	Expansin Engineering Database: A navigation and classification tool for expansins and homologues
Q34254810	Expansion of the APC superfamily of secondary carriers
Q46732325	Experimental analysis of co-evolution within protein complexes: the yeast exosome as a model
Q45137403	Experimental and theoretical studies of the three-dimensional structure of human interleukin-4.
Q71460513	Experimental and theoretical study of electrostatic effects on the isoelectric pH and the pKa of the catalytic residue His-102 of the recombinant ribonuclease from Bacillus amyloliquefaciens (barnase)
Q90516337	Experimental comparison of energy landscape features of ubiquitin family proteins
Q30398313	Experimental conformational energy maps of proteins and peptides
Q36978145	Experimental identification of specificity determinants in the domain linker of a LacI/GalR protein: bioinformatics-based predictions generate true positives and false negatives
Q45070157	Experimental indication for the existence of multiple Trp rotamers in von Willebrand Factor A3 domain
Q28245997	Expert system for predicting protein localization sites in gram-negative bacteria
Q57808067	Explicit and implicit water simulations of a ?-hairpin peptide
Q30580685	Explicit and implicit water simulations of a beta-hairpin peptide
Q42672328	Explicit solvent dynamics and energetics of HIV-1 protease flap opening and closing.
Q51603813	Explicit-chain model of native-state hydrogen exchange: implications for event ordering and cooperativity in protein folding
Q81230764	Exploiting 3D structural templates for detection of metal-binding sites in protein structures
Q30351476	Exploiting heterogeneous sequence properties improves prediction of protein disorder.
Q46059424	Exploiting sequence and structure homologs to identify protein-protein binding sites
Q40068731	Exploration micromechanism of VP35 IID interaction and recognition dsRNA: A molecular dynamics simulation
Q47996335	Exploration of conformational changes in lactose permease upon sugar binding and proton transfer through coarse-grained simulations
Q57000538	Exploration of disorder in protein structures by X-ray restrained molecular dynamics
Q52008629	Exploration of structural features of monomeric helical peptides designed with a genetic algorithm.
Q73798377	Exploration of the S(')(1) subsite of neprilysin: a joined molecular modeling and site-directed mutagenesis study
Q30329266	Exploratory studies of ab initio protein structure prediction: Multiple copy simulated annealing, AMBER energy functions, and a generalized born/solvent accessibility solvation model
Q48042958	Exploring additivity effects of double mutations on the binding affinity of protein-protein complexes.
Q85993131	Exploring alternate states and oligomerization preferences of coiled-coils by de novo structure modeling
Q92474143	Exploring alternative catalytic mechanisms of the Cas9 HNH domain
Q51438298	Exploring c-Met kinase flexibility by sampling and clustering its conformational space.
Q51501233	Exploring conformational changes coupled to ionization states using a hybrid Rosetta‐MCCE protocol
Q51639702	Exploring coumarin egress channels in human cytochrome p450 2a6 by random acceleration and steered molecular dynamics simulations
Q27748821	Exploring hydrophobic sites in proteins with xenon or krypton
Q38953505	Exploring interaction mechanisms of the inhibitor binding to the VP35 IID region of Ebola virus by all atom molecular dynamics simulation method
Q91802564	Exploring molecular mechanism of allosteric inhibitor to relieve drug resistance of multiple mutations in HIV-1 protease by enhanced conformational sampling
Q30343068	Exploring peptide energy landscapes: a test of force fields and implicit solvent models.
Q30559807	Exploring protein interiors: the role of a buried histidine in the KH module fold
Q29617088	Exploring protein native states and large-scale conformational changes with a modified generalized born model
Q90733985	Exploring protein-protein interactions using the site-identification by ligand competitive saturation methodology
Q38463331	Exploring proteome-wide occurrence of clusters of charged residues in eukaryotes
Q34328475	Exploring structural features of the interaction between the scorpion toxinCnErg1 and ERG K+ channels
Q30354348	Exploring structurally conserved solvent sites in protein families.
Q39757341	Exploring structure and interactions of the bacterial adaptor protein YjbH by crosslinking mass spectrometry
Q98830070	Exploring the Effect of Silicene monolayer on the Structure and Function of Villin headpiece and Amyloid fibrils by Molecular dynamics simulations
Q98830095	Exploring the Role of Hydrophilic Amino Acids in Unfolding of Protein in Aqueous Ethanol Solution
Q27765161	Exploring the active site of herpes simplex virus type-1 thymidine kinase by X-ray crystallography of complexes with aciclovir and other ligands
Q52340715	Exploring the binding preferences/specificity in the active site of human cathepsin E.
Q48099827	Exploring the cause of aggregation and reduced Zn binding affinity by G85R mutation in SOD1 rendering amyotrophic lateral sclerosis.
Q51470332	Exploring the charge space of protein-protein association: a proteomic study
Q99627483	Exploring the conformational dynamics of PD1 in complex with different ligands: What we can learn for designing novel PD1 signaling blockers?
Q90556463	Exploring the conformational landscapes of HIV protease structural ensembles using principal component analysis
Q79935403	Exploring the conformational space of protein loops using a mean field technique with MOLS sampling
Q31996404	Exploring the conformational space of protein side chains using dead-end elimination and the A* algorithm
Q77894293	Exploring the dynamic information content of a protein NMR structure: comparison of a molecular dynamics simulation with the NMR and X-ray structures of Escherichia coli ribonuclease HI
Q42217077	Exploring the early stages of the pH-induced conformational change of influenza hemagglutinin
Q47330391	Exploring the effects of sparse restraints on protein structure prediction.
Q73379963	Exploring the energy landscape of a beta hairpin in explicit solvent
Q46297937	Exploring the energy landscapes of molecular recognition by a genetic algorithm: analysis of the requirements for robust docking of HIV-1 protease and FKBP-12 complexes
Q51165258	Exploring the environmental preference of weak interactions in (alpha/beta)8 barrel proteins
Q57014315	Exploring the essential collective dynamics of interacting proteins: Application to prion protein dimers
Q45760615	Exploring the essential collective dynamics of interacting proteins: application to prion protein dimers
Q29618973	Exploring the extremes of sequence/structure space with ensemble fold recognition in the program Phyre
Q87870904	Exploring the free energy landscape of a model β-hairpin peptide and its isoform
Q71774352	Exploring the interaction between D-xylose isomerase and D-xylose by free energy calculation
Q42598180	Exploring the mechanism of DNA polymerases by analyzing the effect of mutations of active site acidic groups in Polymerase β
Q41003035	Exploring the molecular basis of action of ring D aromatic steroidal antiestrogens.
Q46920262	Exploring the molecular basis of heme coordination in human neuroglobin
Q52648484	Exploring the multiscale signaling behavior of phototropin1 from Chlamydomonas reinhardtii using a full-residue space kinetic Monte Carlo molecular dynamics technique
Q46118764	Exploring the origin of the ion selectivity of the KcsA potassium channel
Q51898575	Exploring the protein G helix free-energy surface by solute tempering metadynamics
Q53008295	Exploring the relationship between funneled energy landscapes and two-state protein folding
Q36627376	Exploring the role of large conformational changes in the fidelity of DNA polymerase beta
Q42716014	Exploring the role of structure and dynamics in the function of chymotrypsin inhibitor 2
Q43000327	Exploring the role of the phospholipid ligand in endothelial protein C receptor: a molecular dynamics study.
Q92737879	Exploring the systematic effect of N-substituted PxxP motifs on peptoid affinity to ARHGEF5/TIM SH3 domain and its relationship with ARHGEF5/TIM activation
Q40821867	Exploring the unbinding of Leishmania (L.) amazonensis CPB derived-epitopes from H2 MHC class I proteins
Q46585954	Exploring zipping and assembly as a protein folding principle
Q78627274	Exponential decay kinetics in "downhill" protein folding
Q60602314	Expression and crystallization of the yeast Hsp82 chaperone, and preliminary x-ray diffraction studies of the amino-terminal domain
Q58361093	Expression and crystallization of the yeast Hsp82 chaperone, and preliminary x‐ray diffraction studies of the amino‐terminal domain
Q58868810	Expression in Pichia pastoris and characterization by circular dichroism and NMR of rhodostomin
Q54565093	Expression, crystallization and preliminary X-ray diffraction study of FtsY, the docking protein of the signal recognition particle of E. coli.
Q71671470	Expression, purification, and crystallization of meso-diaminopimelate dehydrogenase from Corynebacterium glutamicum
Q38308577	Expression, purification, and crystallization of restriction endonuclease PvuII with DNA containing its recognition site
Q73134833	Expression, purification, and crystallization of the DNA-binding domain from the Saccharomyces cerevisae cell-cycle transcription factor MBP-1
Q63383688	Expression, purification, and crystallization of the DNA-binding domain from theSaccharomyces cerevisae cell-cycle transcription factor MBP-1
Q73083613	Expression, purification, crystallization, and preliminary X-ray diffraction analysis of the homodimeric bacterial hemoglobin from Vitreoscilla stercoraria
Q33683352	Extending RosettaDock with water, sugar, and pH for prediction of complex structures and affinities for CAPRI rounds 20-27
Q34156490	Extending the PRIME model for protein aggregation to all 20 amino acids
Q36470096	Extension of a protein docking algorithm to membranes and applications to amyloid precursor protein dimerization.
Q68697921	Extension of the fragment method to calculate amino acid zwitterion and side chain partition coefficients
Q73598258	Extent and nature of contacts between protein molecules in crystal lattices and between subunits of protein oligomers
Q46160408	Extent of protein-protein interactions and quasi-equivalence in viral capsids
Q51962070	External cross-validation for unbiased evaluation of protein family detectors: application to allergens.
Q74566120	Extracting contact energies from protein structures: A study using a simplified model
Q30425395	Extracting knowledge from protein structure geometry
Q51072430	Extracting representative structures from protein conformational ensembles.
Q52230744	Extraction of geometrically similar substructures: least-squares and Chebyshev fitting and the difference distance matrix
Q92331388	Extraction of molecular features for the drug discovery targeting protein-protein interaction of Helicobacter pylori CagA and tumor suppressor protein ASSP2
Q43014940	Extreme free energy of stabilization of Taq DNA polymerase
Q36890551	Extreme heat- and pressure-resistant 7-kDa protein P2 from the archaeon Sulfolobus solfataricus is dramatically destabilized by a single-point amino acid substitution
Q91821900	F508del disturbs the dynamics of the nucleotide binding domains of CFTR before and after ATP hydrolysis
Q30349855	FAST: a novel protein structure alignment algorithm.
Q67797012	FASTRUN: a special purpose, hardwired computer for molecular simulation
Q30389832	FF12MC: A revised AMBER forcefield and new protein simulation protocol
Q34694427	FINDSITE‐metal: Integrating evolutionary information and machine learning for structure‐based metal‐binding site prediction at the proteome level
Q51913931	FLIPDock: docking flexible ligands into flexible receptors
Q30383898	FREAD revisited: Accurate loop structure prediction using a database search algorithm.
Q52029632	FROST: a filter-based fold recognition method
Q30351469	FRankenstein becomes a cyborg: the automatic recombination and realignment of fold recognition models in CASP6.
Q31147697	FURSMASA: a new approach to rapid scoring functions that uses a MD-averaged potential energy grid and a solvent-accessible surface area term with parameters GA fit to experimental data
Q30365527	Factors affecting the use of 13C(alpha) chemical shifts to determine, refine, and validate protein structures
Q84544041	Factors determining electrostatic fields in molecular dynamics simulations of the ras/effector interface
Q73798423	Factors determining the relative stability of anionic tetrahedral complexes in serine protease catalysis and inhibition
Q71961401	Factors governing the foldability of proteins
Q74631425	Factors that affect the folding ability of proteins
Q71774356	Failures of inverse folding and threading with gapped alignment
Q30364781	Fams-ace: a combined method to select the best model after remodeling all server models.
Q51635631	Fast accurate evaluation of protein solvent exposure
Q30379190	Fast and accurate automatic structure prediction with HHpred.
Q45028385	Fast and accurate computation of the 13C chemical shifts for an alanine-rich peptide
Q47577731	Fast and accurate modeling of protein-protein interactions by combining template-interface-based docking with flexible refinement
Q30330310	Fast and accurate side-chain topology and energy refinement (FASTER) as a new method for protein structure optimization.
Q80020996	Fast and reliable analysis of molecular motion using proximity relations and dimensionality reduction
Q30335018	Fast and simple Monte Carlo algorithm for side chain optimization in proteins: application to model building by homology
Q42758254	Fast approximations of the rotational diffusion tensor and their application to structural assembly of molecular complexes
Q30382308	Fast assessment of structural models of ion channels based on their predicted current-voltage characteristics.
Q30400754	Fast de novo discovery of low-energy protein loop conformations.
Q42695246	Fast gap-free enumeration of conformations and sequences for protein design
Q30368401	Fast protein tertiary structure retrieval based on global surface shape similarity.
Q30335016	Fast structure alignment for protein databank searching
Q53377930	Fe(2+) binding on amyloid β-peptide promotes aggregation.
Q45957494	Feature selection and classification of protein-protein complexes based on their binding affinities using machine learning approaches.
Q30385361	Feature space resampling for protein conformational search.
Q74093207	Feature-extraction from endopeptidase cleavage sites in mitochondrial targeting peptides
Q54598890	Fermenter production of an artificial fab fragment, rationally designed for the antigen cystatin, and its optimized crystallization through constant domain shuffling.
Q53817763	Ferric uptake regulator protein: binding free energy calculations and per-residue free energy decomposition
Q82538944	Festschrift in honor of the 65th birthday of George D. Rose
Q89950942	FiRES: A computational method for the de novo identification of internal structure similarity in proteins
Q34909306	FiberDock: Flexible induced-fit backbone refinement in molecular docking
Q45965731	FiberID--a technique to identify fibrous protein subclasses.
Q58032981	Fibril elongation mechanisms of HET-s prion-forming domain: Topological evidence for growth polarity
Q83145050	Fibrous long spacing type collagen fibrils have a hierarchical internal structure
Q74460969	Filling a cavity dramatically increases pressure stability of the c-Myb R2 subdomain
Q30324336	Filtered neighbors threading.
Q47659483	Filtering and selection of structural models: combining docking and NMR.
Q30312628	Finding local structural similarities among families of unrelated protein structures: a generic non-linear alignment algorithm
Q46963633	Finding needles in haystacks: Reranking DOT results by using shape complementarity, cluster analysis, and biological information
Q35229098	Finding off-targets, biological pathways, and target diseases for chymase inhibitors via structure-based systems biology approach.
Q92225467	Finding the generalized molecular principles of protein thermal stability
Q47295214	Fine structure of conformational ensembles in adenylate kinase.
Q78140818	Fine tuning the N-terminus of a calcium binding protein: alpha-lactalbumin
Q58322022	Fine tuning the N‐terminus of a calcium binding protein: α‐lactalbumin
Q78955224	Fine-grained protein fold assignment by support vector machines using generalized npeptide coding schemes and jury voting from multiple-parameter sets
Q41616464	Fingerprint‐based structure retrieval using electron density
Q47598103	FireDock: fast interaction refinement in molecular docking
Q24306216	First crystallographic models of human TBC domains in the context of a family-wide structural analysis
Q47810301	First partial three-dimensional model of human monoamine oxidase A
Q44713132	First principles computational study of the active site of arginase
Q27683683	First structural evidence of sequestration of mRNA cap structures by type 1 ribosome inactivating protein from Momordica balsamina
Q71565969	Fitting an inhibitor into the active site of thermolysin: a molecular dynamics case study
Q72635015	Five-stranded beta-sheet sandwiched with two alpha-helices: a structural link between restriction endonucleases EcoRI and EcoRV
Q40766306	Flap flexibility amongst plasmepsins I, II, III, IV, and V: Sequence, structural, and molecular dynamics analyses
Q47700031	Flavors of protein disorder
Q47566942	FlexPepDock lessons from CAPRI peptide-protein rounds and suggested new criteria for assessment of model quality and utility
Q45070169	FlexX-Scan: fast, structure-based virtual screening
Q37406562	Flexibility and charge asymmetry in the activation loop of Src tyrosine kinases
Q45339546	Flexibility and inhibitor binding in cdc25 phosphatases
Q43986872	Flexibility in monomeric Cu,Zn superoxide dismutase detected by limited proteolysis and molecular dynamics simulation.
Q41529085	Flexibility in the N-terminal actin-binding domain: clues from in silico mutations and molecular dynamics.
Q30164240	Flexibility of beta-sheets: principal component analysis of database protein structures
Q81430706	Flexibility of metal binding sites in proteins on a database scale
Q46560922	Flexibility of prolyl oligopeptidase: molecular dynamics and molecular framework analysis of the potential substrate pathways.
Q27728585	Flexibility of the DNA-binding domains of trp repressor
Q36365102	Flexible connection of the N‐terminal domain in ClpB modulates substrate binding and the aggregate reactivation efficiency
Q47625159	Flexible docking allowing induced fit in proteins: insights from an open to closed conformational isomers
Q51168227	Flexible docking and refinement with a coarse-grained protein model using ATTRACT.
Q52230740	Flexible docking using Tabu search and an empirical estimate of binding affinity
Q48046687	Flexible glycine rich motif of Escherichia coli deoxyuridine triphosphate nucleotidohydrolase is important for functional but not for structural integrity of the enzyme
Q41673303	Flexible ligand docking: a multistep strategy approach
Q47615937	Flexible protein alignment and hinge detection
Q51366191	Flexible protein docking refinement using pose-dependent normal mode analysis.
Q46934304	Flexible protein-flexible ligand docking with disrupted velocity simulated annealing.
Q52281044	Flexible protein–ligand docking by global energy optimization in internal coordinates
Q80068370	Flexible relaxation of rigid-body docking solutions
Q44539239	Flexible structural comparison allowing hinge-bending, swiveling motions
Q36386536	Fluctuation dynamics analysis of gp120 envelope protein reveals a topologically based communication network
Q47620132	Fluctuations between stabilizing and destabilizing electrostatic contributions of ion pairs in conformers of the c-Myc-Max leucine zipper
Q47618755	Fluctuations in ion pairs and their stabilities in proteins
Q30393337	Fluctuations of backbone torsion angles obtained from NMR-determined structures and their prediction
Q73233212	Fluorescence quenching in the DsbA protein from Escherichia coli: complete picture of the excited-state energy pathway and evidence for the reshuffling dynamics of the microstates of tryptophan
Q37629401	Fluorescence spectroscopy of soluble E. coli SPase I Δ2-75 reveals conformational changes in response to ligand binding
Q44632570	Fluorescent dyes as probes to study lipid‐binding proteins
Q27731972	Fluoride inhibition of yeast enolase: crystal structure of the enolase-Mg(2+)-F(-)-Pi complex at 2.6 A resolution
Q33225159	Focused library design in GPCR projects on the example of 5-HT(2c) agonists: comparison of structure-based virtual screening with ligand-based search methods
Q57139076	Focusing of electric fields in the active site of Cu-Zn superoxide dismutase: effects of ionic strength and amino-acid modification
Q43741635	Focusing of the electrostatic potential at EF-hands of calbindin D(9k): titration of acidic residues
Q74252601	Fold assignments for amino acid sequences of the CASP2 experiment
Q42431296	Fold homology detection using sequence fragment composition profiles of proteins
Q27678016	Fold of the conserved DTC domain in deltex proteins
Q30424401	Fold recognition and ab initio structure predictions using hidden Markov models and beta-strand pair potentials
Q30969610	Fold recognition and accurate query-template alignment by a combination of PSI-BLAST and threading
Q51945460	Fold recognition and accurate sequence-structure alignment of sequences directing beta-sheet proteins
Q31124129	Fold recognition by combining sequence profiles derived from evolution and from depth-dependent structural alignment of fragments
Q58041659	Fold recognition by concurrent use of solvent accessibility and residue depth
Q40661549	Fold recognition from sequence comparisons.
Q30429641	Fold recognition using predicted secondary structure sequences and hidden Markov models of protein folds
Q52141230	Fold recognition using sequence and secondary structure information.
Q73472701	Fold recognition with minimal gaps
Q44515167	Fold recognition, homology modeling, docking simulations, kinetics analysis and mutagenesis of ATP/CTP:tRNA nucleotidyltransferase from Methanococcus jannaschii
Q30351000	Fold usage on genomes and protein fold evolution.
Q34082277	Fold versus sequence effects on the driving force for protein-mediated electron transfer
Q30390297	FoldGPCR: structure prediction protocol for the transmembrane domain of G protein-coupled receptors from class A.
Q98167046	Foldability and chameleon propensity of fold-switching protein sequences
Q54784061	Folding 19 proteins to their native state and stability of large proteins from a coarse-grained model.
Q52082498	Folding Lennard-Jones proteins by a contact potential
Q46846117	Folding and amyloid-fibril formation for a series of human stefins' chimeras: any correlation?
Q80538508	Folding and dimerization of the ionic peptide EAK 16-IV
Q33540757	Folding and membrane insertion of amyloid-beta (25-35) peptide and its mutants: implications for aggregation and neurotoxicity
Q86175753	Folding and stability of helical bundle proteins from coarse-grained models
Q30672007	Folding and stability of the three-stranded beta-sheet peptide Betanova: insights from molecular dynamics simulations
Q74721951	Folding and stretching in a Go-like model of titin
Q81364384	Folding behavior of chaperonin-mediated substrate protein
Q27666760	Folding determinants of disulfide bond forming protein B explored by solution nuclear magnetic resonance spectroscopy
Q30885873	Folding in lipid membranes (FILM): a novel method for the prediction of small membrane protein 3D structures
Q67543994	Folding in vitro of bovine pancreatic trypsin inhibitor in the presence of proteins of the endoplasmic reticulum
Q81645659	Folding is not required for bilayer insertion: replica exchange simulations of an alpha-helical peptide with an explicit lipid bilayer
Q46857538	Folding mechanism of beta-hairpins studied by replica exchange molecular simulations
Q77314236	Folding mechanism of three structurally similar β-sheet proteins
Q44972885	Folding of RNase T1 is decelerated by a specific tertiary contact in a folding intermediate
Q46635184	Folding of Top7 in unbiased all-atom Monte Carlo simulations.
Q57953582	Folding of a small helical protein using hydrogen bonds and hydrophobicity forces
Q30164156	Folding of beta/alpha-unit scrambled forms of S. cerevisiae triosephosphate isomerase: Evidence for autonomy of substructure formation and plasticity of hydrophobic and hydrogen bonding interactions in core of (beta/alpha)8-barrel.
Q41294766	Folding of bovine growth hormone is consistent with the molten globule hypothesis
Q52068721	Folding of bundles of alpha-helices in solution, membranes, and adsorbed overlayers
Q43565756	Folding of intracellular retinol and retinoic acid binding proteins
Q84789916	Folding of multidomain proteins: Biophysical consequences of tethering even in apparently independent folding
Q44928025	Folding of tandem-linked domains.
Q81489735	Folding pathway dependence on energetic frustration and interaction heterogeneity for a three-dimensional hydrophobic protein model
Q81645663	Folding pathways for initiator and effector procaspases from computer simulations
Q35531140	Folding protein alpha-carbon chains into compact forms by Monte Carlo methods
Q46162407	Folding simulations and computer redesign of protein A three-helix bundle motifs
Q46144488	Folding simulations of Trp-cage mini protein in explicit solvent using biasing potential replica-exchange molecular dynamics simulations
Q89248619	Folding superfunnel to describe cooperative folding of interacting proteins
Q45753777	Folding the ribonuclease H domain of Moloney murine leukemia virus reverse transcriptase requires metal binding or a short N-terminal extension
Q47430850	Folding thermodynamics of three beta-sheet peptides: a model study
Q40940259	Folding thermodynamics of β-hairpins studied by replica-exchange molecular dynamics simulations
Q88781976	Folding with a protein's native shortcut network
Q48602264	Folding with downhill behavior and low cooperativity of proteins
Q52230737	Folding-unfolding energy change of a simple sphere model protein and an energy landscape of the folding process
Q31623630	Folding-unfolding of goat alpha-lactalbumin studied by stopped-flow circular dichroism and molecular dynamics simulations
Q58616280	Folding-unfolding thermodynamics of a ?-heptapeptide from equilibrium simulations
Q74452346	Folding-unfolding thermodynamics of a beta-heptapeptide from equilibrium simulations
Q73365487	For Guldberg and Waage, with love and cratic entropy
Q46683365	Force calculations in automated docking: enzyme-substrate interactions in Fusarium oxysporum Cel7B.
Q54756335	Formation of heterodimers between wild type and mutant trp aporepressor polypeptides of Escherichia coli.
Q43107227	Formation of the RFX gene regulatory complex induces folding of the interaction domain of RFXAP.
Q30352752	Formulation of probabilistic models of protein structure in atomic detail using the reference ratio method.
Q51918735	Four-body contact potentials derived from two protein datasets to discriminate native structures from decoys
Q33709370	Fragment peptide library for classification and functional prediction of proteins
Q81786969	Fragment-based local statistical potentials derived by combining an alphabet of protein local structures with secondary structures and solvent accessibilities
Q56877541	Fragment-based modeling of NAD binding to the catalytic subunits of diphtheria and pertussis toxins
Q39434682	Fragment-based modeling of membrane protein loops: successes, failures, and prospects for the future
Q30733711	Free energetics of rigid body association of ubiquitin binding domains: a biochemical model for binding mediated by hydrophobic interaction.
Q44706733	Free energies of binding of polychlorinated biphenyls to the estrogen receptor from a single simulation
Q57204714	Free energy barrier estimation of unfolding the ?-helical surfactant-associated polypeptide C
Q44496096	Free energy calculations for the relative binding affinity between DNA and lambda-repressor
Q46141636	Free energy calculations on binding and catalysis by alpha-lytic protease: the role of substrate size in the P1 pocket
Q83921867	Free energy calculations show that acidic P1 variants undergo large pKa shifts upon binding to trypsin
Q77360637	Free energy distributions in proteins
Q58429825	Free energy landscape and folding mechanism of a β-hairpin in explicit water: A replica exchange molecular dynamics study
Q79909335	Free energy landscape of a biomolecule in dihedral principal component space: sampling convergence and correspondence between structures and minima
Q28205750	Free energy landscape of protein folding in water: Explicit vs. implicit solvent
Q44784437	Free energy simulations and MM-PBSA analyses on the affinity and specificity of steroid binding to antiestradiol antibody
Q52372238	Free energy simulations: the meaning of the individual contributions from a component analysis
Q47307353	Free energy surfaces of beta-hairpin and alpha-helical peptides generated by replica exchange molecular dynamics with the AGBNP implicit solvent model
Q81576302	Free energy surfaces of miniproteins with a betabetaalpha motif: replica exchange molecular dynamics simulation with an implicit solvation model
Q28274213	Free modeling with Rosetta in CASP6
Q44480412	Free-energy computations identify the mutations required to confer trans-sialidase activity into Trypanosoma rangeli sialidase.
Q62846697	Free-energy function based on an all-atom model for proteins
Q33894160	Free-energy function for discriminating the native fold of a protein from misfolded decoys
Q81489841	Free-energy landscape of kinesin by a realistic lattice model
Q34492990	Free-energy landscape of the GB1 hairpin in all-atom explicit solvent simulations with different force fields: Similarities and differences
Q33419441	Free-energy profiles for ions in the influenza M2-TMD channel
Q44060656	Free-energy simulations of the oxidation of c-terminal methionines in calmodulin
Q30368713	Frequent side chain methyl carbon-oxygen hydrogen bonding in proteins revealed by computational and stereochemical analysis of neutron structures.
Q52004497	From analysis of protein structural alignments toward a novel approach to align protein sequences
Q30157963	From coarse-grain to all-atom: toward multiscale analysis of protein landscapes
Q97534589	From monomer to fibril: Abeta-amyloid binding to Aducanumab antibody studied by Molecular Dynamics simulation
Q27637715	From structure to function: YrbI from Haemophilus influenzae (HI1679) is a phosphatase
Q47596962	From the Mediterranean coast to the shores of Lake Ontario: CAPRI's premiere on the American continent
Q42699012	Frustration-guided motion planning reveals conformational transitions in proteins
Q81312745	Full correlation analysis of conformational protein dynamics
Q27748969	Full-matrix least-squares refinement of lysozymes and analysis of anisotropic thermal motion
Q87286617	Function changing mutations in glucocorticoid receptor evolution correlate with their relevance to mode coupling
Q51151309	Function-based assessment of structural similarity measurements using metal co-factor orientation
Q31101736	Function-dependent clustering of orthologues and paralogues of cyclophilins
Q90564387	Function2Form Bridge-Toward synthetic protein holistic performance prediction
Q91325556	Functional Evolution of Proteins
Q45279397	Functional analysis of CYP2D6.31 variant: homology modeling suggests possible disruption of redox partner interaction by Arg440His substitution.
Q37215081	Functional and computational studies of the ligand-associated metal binding site of beta3 integrins
Q27678009	Functional and structural characterization of a thermostable acetyl esterase from Thermotoga maritima
Q38300126	Functional and structural characterization of the catalytic domain of the starch synthase III from Arabidopsis thaliana.
Q27649293	Functional and structural features of the oxyanion hole in a thermophilic esterase from Alicyclobacillus acidocaldarius
Q38310114	Functional and structural studies of pullulanase from Anoxybacillus sp. LM18-11.
Q81003190	Functional annotation by sequence-weighted structure alignments: statistical analysis and case studies from the Protein 3000 structural genomics project in Japan
Q27626749	Functional aspects of the heme bound hemophore HasA by structural analysis of various crystal forms
Q27642259	Functional assignment based on structural analysis: crystal structure of the yggJ protein (HI0303) of Haemophilus influenzae reveals an RNA methyltransferase with a deep trefoil knot
Q31116991	Functional assignment of MAPK phosphatase domains
Q123181565	Functional characterization of a hypothetical protein (TTHA1873) from Thermus thermophilus
Q47974578	Functional conformational changes of endo-1,4-xylanase II from Trichoderma reesei: a molecular dynamics study
Q57689478	Functional conformational changes of endo-1,4-xylanase II fromTrichoderma reesei: A molecular dynamics study
Q38302702	Functional consequences of exchanging domains between LacI and PurR are mediated by the intervening linker sequence
Q93092048	Functional divergence between evolutionary-related LuxG and Fre oxidoreductases of luminous bacteria
Q34254917	Functional evolution of PLP-dependent enzymes based on active-site structural similarities
Q46931830	Functional evolution within a protein superfamily
Q33233796	Functional grouping based on signatures in protein termini
Q30195530	Functional implications of interleukin-1 beta based on the three-dimensional structure
Q34224344	Functional interaction among catalytic residues in subtilisin BPN'.
Q27938732	Functional interaction of 13 yeast SCF complexes with a set of yeast E2 enzymes in vitro
Q43225812	Functional modes of the regulatory arm of AraC.
Q51818440	Functional motions can be extracted from on‐lattice construction of protein structures
Q77133326	Functional protein domains from the thermally driven motion of polypeptide chains: A proposal
Q59859428	Functional restraints on the patterns of amino acid substitutions: Application to sequence-structure homology recognition
Q44379449	Functional role for Tyr 31 in the catalytic cycle of chicken dihydrofolate reductase
Q28281761	Functional role of a protein foldon--an Omega-loop foldon controls the alkaline transition in ferricytochrome c
Q54261035	Functional roles of amino acid residues involved in forming the alpha-helix-turn-alpha-helix operator DNA binding motif of Tet repressor from Tn10
Q42117358	Functional significance of conserved amino acid residues
Q36381301	Functional tuning of the catalytic residue pKa in a de novo designed esterase.
Q44440703	Functionality maps of binding sites: a multiple copy simultaneous search method
Q54719168	Functionally acceptable substitutions in two alpha-helical regions of lambda repressor.
Q34168536	Functionally important positions can comprise the majority of a protein's architecture
Q37349376	Funnel-like organization in sequence space determines the distributions of protein stability and folding rate preferred by evolution
Q29617521	Funnels, pathways, and the energy landscape of protein folding: a synthesis
Q68082928	Further experimental studies of the disulfide folding transition of ribonuclease A
Q45735421	Further studies of the helix dipole model: effects of a free alpha-NH3+ or alpha-COO- group on helix stability
Q100674232	Further thermo-stabilization of thermophilic rhodopsin from Thermus thermophilus JL-18 through engineering in extramembrane regions
Q30425234	Future directions in folding: the multi-state nature of protein structure
Q52413361	Fuzzy cluster analysis of molecular dynamics trajectories
Q40051800	Fuzzy domains: new way of describing flexibility and interdependence of the protein domains
Q34906286	G protein inactive and active forms investigated by simulation methods
Q38324611	G-protein-coupled receptor domain overexpression in Halobacterium salinarum: long-range transmembrane interactions in heptahelical membrane proteins.
Q52015272	GAPDOCK: a Genetic Algorithm Approach to Protein Docking in CAPRI round 1.
Q38517870	GEMDOCK: a generic evolutionary method for molecular docking.
Q33928362	GGDEF domain is homologous to adenylyl cyclase
Q50643791	GGIP: Structure and sequence-based GPCR-GPCR interaction pair predictor
Q30430082	GLASS: a tool to visualize protein structure prediction data in three dimensions and evaluate their consistency
Q30437388	GPCR 3D homology models for ligand screening: lessons learned from blind predictions of adenosine A2a receptor complex
Q51906608	GRID-MD-A tool for massive simulation of protein channels
Q30417143	GSAFold: A new application of GSA to protein structure prediction
Q42666969	Gain of local structure in an amphipathic peptide does not require a specific tertiary framework.
Q34287670	Gaps in structurally similar proteins: towards improvement of multiple sequence alignment
Q73326566	Gas phase hydrogen/deuterium exchange reactions of peptide ions in a quadrupole ion trap mass spectrometer
Q52405221	Gaussian neighborhood: a new measure of accessibility for residues of protein molecules
Q38510895	Gene ontology functional annotations at the structural domain level
Q90296969	Gene ontology improves template selection in comparative protein docking
Q52981145	General and targeted statistical potentials for protein-ligand interactions
Q85295079	General mean-field theory for mechanical hysteresis of network-like macromolecules
Q37656141	General trends of dihedral conformational transitions in a globular protein
Q32051928	Generalized affine gap costs for protein sequence alignment
Q30328277	Generalized comparative modeling (GENECOMP): a combination of sequence comparison, threading, and lattice modeling for protein structure prediction and refinement.
Q81628609	Generalized correlation for biomolecular dynamics
Q33256084	Generalized modeling of enzyme-ligand interactions using proteochemometrics and local protein substructures
Q30351467	Generalized protein structure prediction based on combination of fold-recognition with de novo folding and evaluation of models.
Q95779344	Generating stereochemically acceptable protein pathways
Q31007257	Generation and analysis of a protein-protein interface data set with similar chemical and spatial patterns of interactions
Q31001554	Generation of a substructure library for the description and classification of protein secondary structure. I. Overview of the methods and results
Q31001600	Generation of a substructure library for the description and classification of protein secondary structure. II. Application to spectra-structure correlations in Fourier transform infrared spectroscopy
Q73472715	Generation of accurate protein loop conformations through low-barrier molecular dynamics
Q27644818	Generation of blood group specificity: new insights from structural studies on the complexes of A- and B-reactive saccharides with basic winged bean agglutinin
Q54718802	Generation of potential structures for the G-domain of chloroplast EF-Tu using comparative molecular modeling.
Q30428160	Generation of pseudonative protein structures for threading
Q34226353	Generic inhibition of amyloidogenic proteins by two naphthoquinone–tryptophan hybrid molecules
Q69364372	Genetic analysis of the molecular basis for beta-adrenergic receptor subtype specificity
Q42524546	Genome wide analysis of pathogenic SH2 domain mutations
Q30358119	Genome-based identification and characterization of a putative mucin-binding protein from the surface of Streptococcus pneumoniae.
Q33187590	Genome-based identification of a carbohydrate binding module in Streptococcus pneumoniae hyaluronate lyase.
Q34353364	Genome-scale prediction of proteins with long intrinsically disordered regions
Q97547556	Genome-wide and structural analyses of pseudokinases encoded in the genome of Arabidopsis thaliana provide functional insights
Q86867268	Genome-wide computational determination of the human metalloproteome
Q51872846	Genome-wide enzyme annotation with precision control: catalytic families (CatFam) databases
Q100694983	Genomic screening and molecular dynamics simulations of cyanovirin-N homologs from Cyanobacteria phylum
Q90411516	Genomic screening of new putative antiviral lectins from Amazonian cyanobacteria based on a bioinformatics approach
Q27658966	Genomics, evolution, and crystal structure of a new family of bacterial spore kinases
Q30410943	Geofold: topology-based protein unfolding pathways capture the effects of engineered disulfides on kinetic stability.
Q77707835	Geometric and chemical patterns of interaction in protein--ligand complexes and their application in docking
Q46194094	Geometric characteristics of hydrogen bonds involving sulfur atoms in proteins
Q39779712	Geometric constraints for porphyrin binding in helical protein binding sites.
Q81682282	Geometric cooperativity and anticooperativity of three-body interactions in native proteins
Q51978830	Geometric preferences of crosslinked protein-derived cofactors reveal a high propensity for near-sequence pairs
Q52276340	Geometric versus topological clustering: an insight into conformation mapping
Q90564490	Geometrical characterization of T cell receptor binding modes reveals class-specific binding to maximize access to antigen
Q30364899	Geometrical comparison of two protein structures using Wigner-D functions.
Q38711042	Geometrical principles of homomeric β-barrels and β-helices: Application to modeling amyloid protofilaments.
Q45962694	Geometrically centered region: A “wet” model of protein binding hot spots not excluding water molecules
Q53671447	Geometry and physics of proteins
Q47606407	Geometry-based flexible and symmetric protein docking
Q51635798	Gibbs adsorption isotherm combined with Monte Carlo sampling to see action of cosolutes on protein folding
Q30380089	Global and local model quality estimation at CASP8 using the scoring functions QMEAN and QMEANclust.
Q42403433	Global and local structural similarity in protein–protein complexes: Implications for template‐based docking
Q33809669	Global fold of human cannabinoid type 2 receptor probed by solid-state 13C-, 15N-MAS NMR and molecular dynamics simulations
Q58048214	Global multiple-sequence alignment with repeats
Q52955479	Global secondary structure packing angle bias in proteins
Q46719735	Glucoamylase structural, functional, and evolutionary relationships
Q35209218	Glucose interactions with a model peptide
Q43644964	Glucose oxidase from Penicillium amagasakiense: characterization of the transition state of its denaturation from molecular dynamics simulations
Q74246354	Glucose-6-phosphate transporter and receptor functions of the glucose 6-phosphatase system analyzed from a consensus defined by multiple alignments
Q58112056	Glutamate Dehydrogenase: Structure of a Hyperinsulinism Mutant, Corrections to the Atomic model, and Insights into a Regulatory Site
Q27649934	Glutathione reductase and thioredoxin reductase at the crossroad: the structure of Schistosoma mansoni thioredoxin glutathione reductase
Q92382744	Glutathione transferase Omega 1-1 (GSTO1-1) modulates Akt and MEK1/2 signaling in human neuroblastoma cell SH-SY5Y
Q27650585	Glutathionylation-triggered conformational changes of glutaredoxin Grx1 from the yeast Saccharomyces cerevisiae
Q46021241	Gly-238-Ser substitution changes the substrate specificity of the SHV class A beta-lactamases.
Q24302229	Glycine N-methyltransferases: a comparison of the crystal structures and kinetic properties of recombinant human, mouse and rat enzymes
Q46770714	Glycogen phosphorylase inhibitors: a free energy perturbation analysis of glucopyranose spirohydantoin analogues
Q91231461	Grafting a short chameleon sequence from αB crystallin into a β-sheet scaffold protein
Q52082495	Graphical method for force analysis: macromolecular mechanics with atomic force microscopy
Q33420576	Graphical models of protein-protein interaction specificity from correlated mutations and interaction data
Q39692552	Great interactions: How binding incorrect partners can teach us about protein recognition and function
Q46721058	Grouping of amino acid types and extraction of amino acid properties from multiple sequence alignments using variance maximization
Q59806983	Growth and analysis of crystal forms of toxic shock syndrome toxin 1
Q50939945	Guanidine hydrochloride denaturation of dopamine-induced α-synuclein oligomers: a small-angle X-ray scattering study
Q52015267	Guided docking: first step to locate potential binding sites
Q30369792	Guiding conformation space search with an all-atom energy potential.
Q64018874	H-bond network optimization in protein-protein complexes: Are all-atom force field scores enough?
Q29615981	HADDOCK versus HADDOCK: new features and performance of HADDOCK2.0 on the CAPRI targets
Q30419365	HERA--a program to draw schematic diagrams of protein secondary structures
Q77751671	HIKE, a candidate protein binding site for PH domains, is a major regulatory region of Gbeta proteins
Q42064637	HIV-1 protease function and structure studies with the simplicial neighborhood analysis of protein packing method
Q45730318	HIVdb: a database of the structures of human immunodeficiency virus protease
Q37063734	HIV‐1 ENV gp120 structural determinants for peptide triazole dual receptor site antagonism
Q34324246	HOOK: a program for finding novel molecular architectures that satisfy the chemical and steric requirements of a macromolecule binding site
Q54094052	Hallmarks of mycolic acid biosynthesis: a comparative genomics study
Q51034898	Hamiltonian replica exchange combined with elastic network analysis to enhance global domain motions in atomistic molecular dynamics simulations
Q52043306	Hamming distance geometry of a protein conformational space: application to the clustering of a 4-ns molecular dynamics trajectory of the HIV-1 integrase catalytic core
Q30429623	Handling context‐sensitivity in protein structures using graph theory: Bona fide prediction
Q123016270	Happy birthday michael rossmann
Q71537029	Hard alpha-keratin IF: a structural model lacking a head-to-tail molecular overlap but having hybrid features characteristic of both epidermal keratin and vimentin IF
Q70980716	Harmonicity and anharmonicity in protein dynamics: a normal mode analysis and principal component analysis
Q44334205	Helical fold prediction for the cyclin box.
Q62141728	Helical preferences of alanine, glycine, and aminoisobutyric homopeptides
Q53868514	Helicobacter pylori protein HP0222 belongs to Arc/MetJ family of transcriptional regulators
Q50461500	Helix formation is a dynamical bottleneck in the recovery reaction of Photoactive Yellow Protein
Q30360293	Helix kinks are equally prevalent in soluble and membrane proteins.
Q47644752	Helix lap-joints as ion-binding sites: DNA-binding motifs and Ca-binding "EF hands" are related by charge and sequence reversal
Q30969625	Helix nucleation kinetics from molecular simulations in explicit solvent
Q57000496	Helix packing in proteins: Prediction and energetic analysis of dimeric, trimeric, and tetrameric GCN4 coiled coil structures
Q68115170	Helix packing of leucine-rich peptides: a parallel leucine ladder in the structure of Boc-Aib-Leu-Aib-Aib-Leu-Leu-Leu-Aib-Leu-Aib-OMe
Q43219182	Helix propensities calculations for amino acids in alanine based peptides using Jarzynski's equality
Q30332484	Helix propensities of short peptides: molecular dynamics versus bioinformatics.
Q42957108	Helix stability of oligoglycine, oligoalanine, and oligo-β-alanine dodecamers reflected by hydrogen-bond persistence
Q43495944	Helix-capping interaction in lambda Cro protein: a free energy simulation analysis.
Q46426339	Helix-coil transition of alanine peptides in water: force field dependence on the folded and unfolded structures
Q57906347	Helix-forming tendencies of nonpolar amino acids predicted by Monte Carlo simulated annealing
Q46863114	Helix-helix packing angle preferences for finite helix axes
Q30386084	Helix-sheet packing in proteins
Q43825559	Helix‐coil transition of PrP106–126: Molecular dynamic study
Q58036768	Helix‐helix packing angle preferences for finite helix axes
Q45736215	Heme proteins--diversity in structural characteristics, function, and folding
Q57088191	Hemoglobins from deep-sea hydrothermal vent scaleworms of the genus Branchipolynoe: a new type of quaternary structure
Q41209193	Heptad breaks in alpha-helical coiled coils: stutters and stammers
Q74015810	Heralding EarlyView(R)!
Q46249676	Heterogeneity of single molecule FRET signals reveals multiple active ribosome subpopulations
Q27658969	Heterologous quaternary structure of CXCL12 and its relationship to the CC chemokine family
Q67936538	Hexamers of subunit II from Limulus hemocyanin (a 48-mer) have the same quaternary structure as whole Panulirus hemocyanin molecules
Q46468378	Hidden Markov models that use predicted local structure for fold recognition: alphabets of backbone geometry
Q57209050	Hidden Markov models that use predicted secondary structures for fold recognition
Q57209072	Hidden Markov models that use predicted secondary structures for fold recognition
Q44322008	Hidden order in the GroEL-GroES-(ADP)7 chaperonin: forms, folding, and ADP-binding sites
Q61836185	Hidden partners: Using cross-docking calculations to predict binding sites for proteins with multiple interactions
Q30371326	Hierarchical domain-motion analysis of conformational changes in sarcoplasmic reticulum Ca²⁺-ATPase.
Q30332658	Hierarchical protein folding pathways: a computational study of protein fragments.
Q104111721	Hierarchical,rotation-equivariant neural networks to select structural models of protein complexes
Q43825571	Hierarchy of simulation models in predicting molecular recognition mechanisms from the binding energy landscapes: structural analysis of the peptide complexes with SH2 domains.
Q97591243	High Resolution Structure of A Partially Folded Insulin Aggregation Intermediate
Q51505896	High accuracy prediction of beta-turns and their types using propensities and multiple alignments
Q33300265	High accuracy template based modeling by global optimization
Q38333671	High affinity fucose binding of Pseudomonas aeruginosa lectin PA-IIL: 1.0 A resolution crystal structure of the complex combined with thermodynamics and computational chemistry approaches
Q80539443	High incidence of ubiquitin-like domains in human ubiquitin-specific proteases
Q60430668	High performance liquid chromatography-electrospray mass spectrometry for the simultaneous resolution and identification of intrinsic thylakoid membrane proteins
Q30423793	High pressure effects on protein structure and function
Q61963718	High pressure reveals structural determinants for globin hexacoordination: Neuroglobin and myoglobin cases
Q51899066	High quality binding modes in docking ligands to proteins
Q27646756	High resolution X-ray crystallographic structure of bovine heart cytochrome c and its application to the design of an electron transfer biosensor
Q27689471	High resolution crystal structure of Clostridium propionicum β-alanyl-CoA:ammonia lyase, a new member of the "hot dog fold" protein superfamily
Q27682725	High resolution crystal structure of Sco5413, a widespread actinomycete MarR family transcriptional regulator of unknown function
Q27683599	High resolution crystal structure of dengue-3 envelope protein domain III suggests possible molecular mechanisms for serospecific antibody recognition
Q56815822	High resolution crystal structure of deoxy hemoglobin from Trematomus bernacchii at different pH values: The role of histidine residues in modulating the strength of the root effect
Q58859642	High resolution crystal structures of unliganded and liganded human liver ACBP reveal a new mode of binding for the acyl-CoA ligand
Q73319271	High resolution fast quantitative docking using Fourier domain correlation techniques
Q43026640	High resolution structure and sequence of T. aurantiacus xylanase I: implications for the evolution of thermostability in family 10 xylanases and enzymes with (beta)alpha-barrel architecture
Q80011294	High resolution structure of streptavidin in complex with a novel high affinity peptide tag mimicking the biotin binding motif
Q30984706	High throughput docking for library design and library prioritization
Q30393908	High-accuracy modeling of antibody structures by a search for minimum-energy recombination of backbone fragments
Q91142474	High-accuracy protein structures by combining machine-learning with physics-based refinement
Q92039581	High-accuracy refinement using Rosetta in CASP13
Q33635681	High-precision measurement of hydrogen bond lengths in proteins by nuclear magnetic resonance methods
Q90299958	High-resolution crystal structure of peptidyl-tRNA hydrolase from Thermus thermophilus
Q40426555	High-resolution crystal structures leverage protein binding affinity predictions.
Q39205310	High-resolution modeling of antibody structures by a combination of bioinformatics, expert knowledge, and molecular simulations
Q47867048	High-resolution prediction of protein helix positions and orientations
Q27757666	High-resolution solution structure of Bacillus subtilis IIAglc
Q57078252	High-resolution solution structure ofBacillus subtilis IIAglc
Q27640183	High-resolution structure and biochemical properties of a recombinant Proteus mirabilis catalase depleted in iron
Q27618775	High-resolution structures of scytalone dehydratase-inhibitor complexes crystallized at physiological pH
Q57818558	High-resolution structures of scytalone dehydratase-inhibitor complexes crystallized at physiological pH
Q56992809	High-throughput prediction of disordered moonlighting regions in protein sequences
Q30369215	Highly accurate method for ligand-binding site prediction in unbound state (apo) protein structures.
Q27658105	Highly conserved glycine 86 and arginine 87 residues contribute differently to the structure and activity of the mature HIV-1 protease
Q73964867	Highly constrained multiple-copy refinement of protein crystal structures
Q44243757	Highly covarying residues have a functional role in antibody constant domains
Q48626094	Hiking in the energy landscape in sequence space: a bumpy road to good folders
Q52322021	Hinge-bending motion in citrate synthase arising from normal mode calculations
Q38456853	HingeMaster: normal mode hinge prediction approach and integration of complementary predictors.
Q28248187	HingeProt: automated prediction of hinges in protein structures
Q42112965	Histidine in continuum electrostatics protonation state calculations
Q43256876	Holo-BtuF stabilizes the open conformation of the vitamin B12 ABC transporter BtuCD.
Q72335570	Homologous modeling of the lysosomal protective protein/carboxypeptidase L: structural and functional implications of mutations identified in galactosialidosis patients
Q87476848	Homologous steroid receptors assemble at identical promoter architectures with unique energetics of cooperativity
Q30305513	Homologs of the alpha- and beta-subunits of mammalian brain platelet-activating factor acetylhydrolase Ib in the Drosophila melanogaster genome
Q28303882	Homology model for the human GSTT2 Theta class glutathione transferase
Q41607233	Homology model of juvenile hormone esterase from the crop pest, Heliothis virescens
Q47972593	Homology model of the human tRNA splicing ligase RtcB.
Q36087159	Homology modeling and molecular dynamics simulations of the active state of the nociceptin receptor reveal new insights intoagonist binding and activation
Q42618746	Homology modeling and molecular dynamics simulations of the alpha1 glycine receptor reveals different states of the channel
Q33863107	Homology modeling and molecular dynamics simulations of the glycine receptor ligand binding domain
Q40470015	Homology modeling and molecular dynamics study of West Nile virus NS3 protease: a molecular basis for the catalytic activity increased by the NS2B cofactor.
Q41705444	Homology modeling and substrate binding study of human CYP2C18 and CYP2C19 enzymes
Q41705437	Homology modeling and substrate binding study of human CYP2C9 enzyme
Q28137614	Homology modeling and substrate binding study of human CYP4A11 enzyme
Q29031204	Homology modeling and substrate binding study of human CYP4A11 enzyme
Q30424405	Homology modeling by the ICM method
Q52229477	Homology modeling of an RNP domain from a human RNA-binding protein: Homology-constrained energy optimization provides a criterion for distinguishing potential sequence alignments
Q46524377	Homology modeling of histidine-containing phosphocarrier protein and eosinophil-derived neurotoxin: construction of models and comparison with experiment
Q73205395	Homology modeling of rabbit prolactin hormone complexed with its receptor
Q30193943	Homology modeling of the Abl-SH3 domain.
Q74252568	Homology modeling with internal coordinate mechanics: Deformation zone mapping and improvements of models via conformational search
Q79307159	Homology models of dipeptidyl peptidases 8 and 9 with a focus on loop predictions near the active site
Q41870119	Homology models of the HIV-1 attachment inhibitor BMS-626529 bound to gp120 suggest a unique mechanism of action
Q46007965	Homology models of two isozymes of manganese peroxidase: prediction of a Mn(II) binding site.
Q69058504	Homology of lysosomal enzymes and related proteins: prediction of posttranslational modification sites including phosphorylation of mannose and potential epitopic and substrate binding sites in the alpha- and beta-subunits of hexosaminidases, alpha-
Q38342633	Hormone phage: an enrichment method for variant proteins with altered binding properties
Q40565690	Host-guest scale of left-handed polyproline II helix formation.
Q36839286	Hot spots--a review of the protein-protein interface determinant amino-acid residues
Q27690810	Hot-spot analysis to dissect the functional protein-protein interface of a tRNA-modifying enzyme
Q85076877	How T cell receptors interact with peptide‐MHCs: A multiple steered molecular dynamics study
Q33763840	How a small change in retinal leads to G-protein activation: initial events suggested by molecular dynamics calculations
Q88781994	How accurately do force fields represent protein side chain ensembles?
Q45395599	How calcium inhibits the magnesium-dependent kinase gsk3β: a molecular simulation study
Q44711034	How catalase recognizes H₂O₂ in a sea of water
Q51660327	How different from random are docking predictions when ranked by scoring functions?
Q40191460	How do side chains orient globally in protein structures?
Q43014738	How do thermophilic proteins resist aggregation?
Q47816987	How does nitrous oxide reductase interact with its electron donors?--A docking study
Q38610833	How fast monoamine oxidases decompose adrenaline? Kinetics of isoenzymes A and B evaluated by empirical valence bond simulation
Q42634689	How general is the nucleation-condensation mechanism?
Q93059658	How good are comparative models in the understanding of protein dynamics?
Q37601847	How good is automated protein docking?
Q43594673	How good is prediction of protein structural class by the component-coupled method?
Q30356549	How inaccuracies in protein structure models affect estimates of protein-ligand interactions: computational analysis of HIV-I protease inhibitor binding.
Q38322199	How maltose influences structural changes to bind to maltose-binding protein: results from umbrella sampling simulation
Q71774362	How many fold types of protein are there in nature?
Q34035641	How many ionizable groups can sit on a protein hydrophobic core?
Q30411400	How noise in force fields can affect the structural refinement of protein models?
Q51663923	How orientational order governs collectivity of folded proteins
Q30362362	How the folding rates of two- and multistate proteins depend on the amino acid properties.
Q93026413	How to choose templates for modeling of protein complexes: Insights from benchmarking template-based docking
Q30327152	How to generate improved potentials for protein tertiary structure prediction: a lattice model study.
Q31922968	How to guarantee optimal stability for most representative structures in the Protein Data Bank.
Q31143562	How to lose a kink and gain a helix: pH independent conformational changes of the fusion domains from influenza hemagglutinin in heterogeneous lipid bilayers
Q52937569	How well are protein structures annotated in secondary databases?
Q30333271	How well can we predict native contacts in proteins based on decoy structures and their energies?
Q44216908	Human DEAD-box ATPase DDX3 shows a relaxed nucleoside substrate specificity
Q81614114	Human FEZ1 has characteristics of a natively unfolded protein and dimerizes in solution
Q107273003	Human SARS CoV-2 spike protein mutations
Q45028378	Human SARS-coronavirus RNA-dependent RNA polymerase: activity determinants and nucleoside analogue inhibitors
Q30393220	Human and server docking prediction for CAPRI round 30-35 using LZerD with combined scoring functions
Q31151707	Human interleukin-23 receptor antagonists derived from an albumin-binding domain scaffold inhibit IL-23-dependent ex vivo expansion of IL-17-producing T-cells
Q28281160	Human myeloperoxidase and thyroid peroxidase, two enzymes with separate and distinct physiological functions, are evolutionarily related members of the same gene family
Q90307942	Human telomerase protein: Understanding how the catalytic activity is suppressed under single substitutions of some conserved residues. A computational study
Q24300503	Human uroporphyrinogen III synthase: NMR-based mapping of the active site
Q28115413	Human α-amino-β-carboxymuconate-ε-semialdehyde decarboxylase (ACMSD): a structural and mechanistic unveiling
Q28249671	Hundreds of ankyrin-like repeats in functionally diverse proteins: mobile modules that cross phyla horizontally?
Q33310030	Huntingtin interacting protein HYPK is intrinsically unstructured
Q46259165	Hybrid immunoglobulin isotypes of identical specificity produced by genetic recombination in Escherichia coli and expression in lymphoid cells
Q51969053	Hybrid native partitioning of interactions among nonconserved residues in chimeric proteins
Q57814868	Hydration energy landscape of the active site cavity in cytochrome P450cam
Q57814879	Hydration energy landscape of the active site cavity in cytochrome P450cam
Q78854500	Hydration in proteins observed by high-resolution neutron crystallography
Q31106691	Hydration of a hydrophobic cavity and its functional role: a simulation study of human interleukin-1beta.
Q51648439	Hydration of an alpha-helical peptide: comparison of theory and molecular dynamics simulation
Q57875457	Hydration of an α‐Helical peptide: comparison of theory and molecular dynamics simulation
Q81692270	Hydration of protein-protein interfaces
Q47554434	Hydrodynamic Radius Coincides with the Slip Plane Position in the Electrokinetic Behavior of Lysozyme.
Q72511006	Hydrogen bond strength and beta-sheet propensities: the role of a side chain blocking effect
Q81624613	Hydrogen bonding increases packing density in the protein interior
Q57976334	Hydrogen bonding is the prime determinant of carboxyl pKa values at the N-termini of α-helices
Q74614429	Hydrogen bonds between short polar side chains and peptide backbone: prevalence in proteins and effects on helix-forming propensities
Q30362217	Hydrogen bonds involving sulfur atoms in proteins.
Q44184711	Hydrogen exchange in native and denatured states of hen egg-white lysozyme
Q74015797	Hydrogen exchange study of canine milk lysozyme: stabilization mechanism of the molten globule
Q38243902	Hydrolysis of GTP by the alpha-chain of Gs and other GTP binding proteins
Q92354244	Hydrolysis of homocysteine thiolactone results in the formation of Protein-Cys-S-S-homocysteinylation
Q44411429	Hydrolysis of organophosphate compounds by mutant butyrylcholinesterase: A story of two histidines
Q73365493	Hydrophilicity of cavities in proteins
Q43446796	Hydrophobic clustering in nonnative states of a protein: interpretation of chemical shifts in NMR spectra of denatured states of lysozyme
Q80474195	Hydrophobic clusters in protein structures
Q47430831	Hydrophobic complementarity in protein-protein docking
Q52364814	Hydrophobic docking: a proposed enhancement to molecular recognition techniques
Q73256212	Hydrophobic dye inhibits aggregation of molten carbonic anhydrase during thermal unfolding and refolding
Q43017457	Hydrophobic environment is a key factor for the stability of thermophilic proteins
Q30365005	Hydrophobic interactions and ionic networks play an important role in thermal stability and denaturation mechanism of the porcine odorant-binding protein.
Q52007584	Hydrophobic moments of tertiary protein structures
Q73510588	Hydrophobic patches on protein subunit interfaces: characteristics and prediction
Q71623229	Hydrophobic patches on the surfaces of protein structures
Q47554440	Hydrophobic residues can identify native protein structures
Q51327053	Hydrophobic tail length plays a pivotal role in amyloid beta (25-35) fibril-surfactant interactions
Q45279356	Hydrophobic tendency of polar group hydration as a major force in type I antifreeze protein recognition
Q73393596	Hydrophobicity at the surface of proteins
Q43537136	Hydrophobicity of amino acid subgroups in proteins
Q39055069	Hydroxynitrile lyase from Hevea brasiliensis: molecular characterization and mechanism of enzyme catalysis
Q38323950	Hypocrea jecorina (Trichoderma reesei) Cel7A as a molecular machine: A docking study.
Q30380936	I-TASSER: fully automated protein structure prediction in CASP8
Q46664729	ICM-DISCO docking by global energy optimization with fully flexible side-chains
Q129148214	III. Geometrical framework for thinking about globular proteins: Turns in proteins
Q52245934	IMPALA: A simple restraint field to simulate the biological membrane in molecular structure studies
Q51910632	Ideal amino acid exchange forms for approximating substitution matrices
Q52070055	Identification and ab initio simulations of early folding units in proteins
Q52302222	Identification and analysis of long-range electrostatic effects in proteins by computer modeling:aspartate transcarbamylase
Q58882307	Identification and characterization of folding inhibitors of hen egg lysozyme: An example of a new paradigm of drug design
Q33212902	Identification and distribution of protein families in 120 completed genomes using Gene3D.
Q47597557	Identification and functional characterization of the bile acid transport proteins in non-mammalian ileum and mammalian liver
Q38649778	Identification and functionality prediction of pathogenesis-related protein 1 from legume family
Q27646876	Identification and structural characterization of heme binding in a novel dye-decolorizing peroxidase, TyrA
Q34164671	Identification of CCR2‐binding features in Cytl1 by a CCL2‐like chemokine model
Q40178550	Identification of FAKTS as a novel 14-3-3-associated nuclear protein
Q91337711	Identification of FDA-approved drugs as novel allosteric inhibitors of human executioner caspases
Q40317285	Identification of GATC- and CCGG-recognizing Type II REases and their putative specificity-determining positions using Scan2S--a novel motif scan algorithm with optional secondary structure constraints
Q97591131	Identification of Potential Allosteric Binding Sites in Cathepsin K Based on Intramolecular Communication
Q27683617	Identification of a cation transport pathway in Neisseria meningitidis PorB
Q48277571	Identification of a conserved 8 aa insert in the PIP5K protein in the Saccharomycetaceae family of fungi and the molecular dynamics simulations and structural analysis to investigate its potential functional role
Q36816170	Identification of a decapeptide with the binding reactivity for tumor-associated TAG72 antigen from a phage displayed library
Q48022764	Identification of a dimeric KDG aldolase from Agrobacterium tumefaciens
Q27651947	Identification of a key element for hydrogen-bonding patterns between protein kinases and their inhibitors
Q91244973	Identification of a new nucleotide binding site by structural alignment and site directed mutagenesis
Q51121910	Identification of a new subfamily of HNH nucleases and experimental characterization of a representative member, HphI restriction endonuclease
Q41586108	Identification of a novel carbohydrate esterase from Bjerkandera adusta: structural and function predictions through bioinformatics analysis and molecular modeling
Q52043309	Identification of a novel class in the alpha/beta hydrolase fold superfamily: the N-myc differentiation-related proteins
Q27683600	Identification of a novel ligand binding site in phosphoserine phosphatase from the hyperthermophilic archaeon Thermococcus onnurineus
Q30423790	Identification of a pattern in protein structure based on energetic and statistical considerations
Q38333952	Identification of amino acids important for target recognition by the DNA:m5C methyltransferase M.NgoPII by alanine-scanning mutagenesis of residues at the protein-DNA interface
Q36278766	Identification of bacterial guanylate cyclases
Q88064459	Identification of bacterial guanylate cyclases
Q27666649	Identification of biochemical and putative biological role of a xenolog from Escherichia coli using structural analysis
Q95659863	Identification of biochemically neutral positions in liver pyruvate kinase
Q42621319	Identification of common structural features of binding sites in galactose-specific proteins
Q45787056	Identification of critical contact residues in the NC41 epitope of a subtype N9 influenza virus neuraminidase.
Q30350425	Identification of domains and domain interface residues in multidomain proteins from graph spectral method.
Q44689605	Identification of efflux proteins using efficient radial basis function networks with position-specific scoring matrices and biochemical properties
Q38514126	Identification of family determining residues in Jumonji-C lysine demethylases: A sequence-based, family wide classification
Q77435974	Identification of functional and unfolding motions of cutinase as obtained from molecular dynamics computer simulations
Q54608497	Identification of functional motions in the adenylate kinase (ADK) protein family by computational hybrid approaches.
Q44544342	Identification of functionally conserved residues with the use of entropy-variability plots
Q46628068	Identification of fungal oxaloacetate hydrolyase within the isocitrate lyase/PEP mutase enzyme superfamily using a sequence marker-based method
Q30321831	Identification of homologous core structures.
Q51531543	Identification of imine reductase-specific sequence motifs
Q30578492	Identification of mycobacterial lectins from genomic data
Q51918597	Identification of near-native structures by clustering protein docking conformations
Q30357239	Identification of new claudin family members by a novel PSI-BLAST based approach with enhanced specificity.
Q43558040	Identification of new repeating motifs in titin
Q33280444	Identification of novel fragment compounds targeted against the pY pocket of v-Src SH2 by computational and NMR screening and thermodynamic evaluation
Q40098311	Identification of novel host defense peptides and the absence of alpha-defensins in the bovine genome
Q31001610	Identification of novel peptide antagonists for GPIIb/IIIa from a conformationally constrained phage peptide library
Q44124797	Identification of peptide hormones of the amphipathic helix class using the helical hydrophobic moment algorithm
Q56901060	Identification of protein fold and catalytic residues of gamma-hexachlorocyclohexane dehydrochlorinase LinA
Q62274623	Identification of protein fold and catalytic residues of γ-hexachlorocyclohexane dehydrochlorinase LinA
Q30403374	Identification of protein folds: matching hydrophobicity patterns of sequence sets with solvent accessibility patterns of known structures
Q51617488	Identification of protein functional surfaces by the concept of a split pocket
Q24321382	Identification of proteins interacting with protein arginine methyltransferase 8: the Ewing sarcoma (EWS) protein binds independent of its methylation state
Q42623582	Identification of protons position in acid-base enzyme catalyzed reactions: the hepatitis C viral NS3 protease
Q54322060	Identification of putative unfolding intermediates of the mutant His-107-tyr of human carbonic anhydrase II in a multidimensional property space
Q81786978	Identification of putative, stable binding regions through flexibility analysis of HIV-1 gp120
Q82054931	Identification of selectivity-determining residues in cytochrome P450 monooxygenases: a systematic analysis of the substrate recognition site 5
Q84194113	Identification of specificity and promiscuity of PDZ domain interactions through their dynamic behavior
Q47623426	Identification of structural domains in proteins by a graph heuristic
Q34049800	Identification of structural motifs from protein coordinate data: secondary structure and first-level supersecondary structure
Q43920606	Identification of structural proteins from shrimp white spot syndrome virus (WSSV) by 2DE-MS.
Q44060634	Identification of the N-terminal functional domains of Cdk5 by molecular truncation and computer modeling
Q51464727	Identification of the active site of human mitochondrial malonyl-coenzyme a decarboxylase: A combined computational study
Q27678066	Identification of the bile salt binding site on IpaD from Shigella flexneri and the influence of ligand binding on IpaD structure.
Q28492381	Identification of the bona fide DHDPS from a common plant pathogen
Q30333119	Identification of the domains for DNA binding and transactivation function of C protein from bacteriophage Mu.
Q77924671	Identification of the ligand binding site in Fas (CD95) and analysis of Fas-ligand interactions
Q27655403	Identification of trypsin-inhibitory site and structure determination of human SPINK2 serine proteinase inhibitor
Q40880012	Identification of universal selectivity-determining positions in cytochrome P450 monooxygenases by systematic sequence-based literature mining
Q24624622	Identification, analysis, and prediction of protein ubiquitination sites
Q27681687	Identification, structural, and biochemical characterization of a group of large Csn2 proteins involved in CRISPR‐mediated bacterial immunity
Q51495484	Identifying continuous pores in protein structures with PROPORES by computational repositioning of gating residues
Q30356403	Identifying cysteines and histidines in transition-metal-binding sites using support vector machines and neural networks.
Q80445463	Identifying folding nucleus based on residue contact networks of proteins
Q33276607	Identifying long-range structure in the intrinsically unstructured transactivation domain of p53.
Q30376344	Identifying native-like protein structures with scoring functions based on all-atom ECEPP force fields, implicit solvent models and structure relaxation
Q40106053	Identifying novel peroxisomal proteins
Q42055275	Identifying polymer-forming SAM domains
Q30655261	Identifying protein complexes from heterogeneous biological data
Q77926218	Identifying proteins of high designability via surface-exposure patterns
Q30367305	Identifying stabilizing key residues in proteins using interresidue interaction energy matrix.
Q54734467	Illuminating the early signaling pathway of a fungal light-oxygen-voltage photoreceptor.
Q48007546	Immunoglobulin kappa light chain and its amyloidogenic mutants: a molecular dynamics study
Q58175518	Impact of Cl and Na ions on simulated structure and dynamics of βARK1 PH domain
Q58175544	Impact of Cl- and Na+ ions on simulated structure and dynamics of betaARK1 PH domain
Q51934736	Impact of EGFR point mutations on the sensitivity to gefitinib: insights from comparative structural analyses and molecular dynamics simulations
Q42734341	Impact of calcium on N1 influenza neuraminidase dynamics and binding free energy
Q44540221	Impact of deglycosylation and thermal stress on conformational stability of a full length murine igG2a monoclonal antibody: Observations from molecular dynamics simulations
Q44125127	Impact of incorporating the 2C5 crystal structure into comparative models of cytochrome P450 2D6.
Q34442775	Impact of sequence on the molecular assembly of short amyloid peptides
Q34159813	Impact of the K24N mutation on the transactivation domain of p53 and its binding to murine double-minute clone 2
Q57577545	Impact of the tail and mutations G131V and M129V on prion protein flexibility
Q44001444	Implications of structural genomics target selection strategies: Pfam5000, whole genome, and random approaches
Q51909159	Implicit flexibility in protein docking: cross-docking and local refinement
Q57134555	Implicit solvent models for flexible protein-protein docking by molecular dynamics simulation
Q45194411	Implicit solvent simulations of peptide interactions with anionic lipid membranes
Q52206843	Importance of anchor group positioning in protein loop prediction
Q30164075	Importance of hydrophobic cluster formation through long-range contacts in the folding transition state of two-state proteins
Q51092685	Importance of polarization effect in the study of metalloproteins: application of polarized protein specific charge scheme in predicting the reduction potential of azurin
Q47422764	Importance of sequence specificity for predicting protein folding pathways: Perturbed Gaussian chain model
Q30323185	Improved ab initio predictions with a simplified, flexible geometry model.
Q30357341	Improved beta-protein structure prediction by multilevel optimization of nonlocal strand pairings and local backbone conformation.
Q52393861	Improved calculations of compactness and a reevaluation of continuous compact units
Q30382585	Improved de novo structure prediction in CASP11 by incorporating coevolution information into Rosetta.
Q42091603	Improved energy bound accuracy enhances the efficiency of continuous protein design
Q51168223	Improved flexible refinement of protein docking in CAPRI rounds 22-27.
Q30155964	Improved identification of outer membrane beta barrel proteins using primary sequence, predicted secondary structure, and evolutionary information
Q30429060	Improved method for prediction of protein backbone U-turn positions and major secondary structural elements between U-turns
Q46284437	Improved model building and assessment of the Calcium-sensing receptor transmembrane domain
Q63191335	Improved modeling of side-chains in proteins with rotamer-based methods: A flexible rotamer model
Q47711925	Improved performance in CAPRI round 37 using LZerD docking and template-based modeling with combined scoring functions
Q38701850	Improved prediction for N-termini of alpha-helices using empirical information
Q40921781	Improved prediction for the structure of the dimeric transmembrane domain of glycophorin A obtained through global searching
Q56877803	Improved prediction for the structure of the dimeric transmembrane domain of glycophorin A obtained through global searching
Q24634442	Improved prediction of protein side-chain conformations with SCWRL4
Q45945716	Improved protein contact predictions with the MetaPSICOV2 server in CASP12.
Q62846812	Improved protein free energy calculation by more accurate treatment of nonbonded energy: Application to chymotrypsin inhibitor 2, V57A
Q52245930	Improved protein free energy calculation by more accurate treatment of nonbonded energy: application to chymotrypsin inhibitor 2, V57A.
Q50420082	Improved protein model quality assessments by changing the target function.
Q29616787	Improved protein-ligand docking using GOLD
Q56999449	Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins
Q45003124	Improved sequence-based prediction of protein secondary structures by combining vacuum-ultraviolet circular dichroism spectroscopy with neural network
Q24616749	Improved side-chain torsion potentials for the Amber ff99SB protein force field
Q27642890	Improved thermostability of bacillus circulans cyclodextrin glycosyltransferase by the introduction of a salt bridge
Q73083584	Improvement of protein secondary structure prediction using binary word encoding
Q51956434	Improvement of statistical potentials and threading score functions using information maximization
Q46568966	Improving CAPRI predictions: optimized desolvation for rigid-body docking
Q27652286	Improving NMR protein structure quality by Rosetta refinement: A molecular replacement study
Q30370764	Improving accuracy and efficiency of blind protein-ligand docking by focusing on predicted binding sites.
Q30369974	Improving accuracy of protein contact prediction using balanced network deconvolution.
Q34683409	Improving computational protein design by using structure-derived sequence profile
Q30361622	Improving fragment quality for de novo structure prediction.
Q34612025	Improving physical realism, stereochemistry, and side-chain accuracy in homology modeling: Four approaches that performed well in CASP8.
Q30399508	Improving prediction of helix-helix packing in membrane proteins using predicted contact numbers as restraints
Q45747432	Improving ranking of models for protein complexes with side chain modeling and atomic potentials
Q48650559	Improving taxonomy-based protein fold recognition by using global and local features.
Q52234205	Improving the accuracy of protein pKa calculations: conformational averaging versus the average structure
Q39323801	Improving the accuracy of protein stability predictions with multistate design using a variety of backbone ensembles
Q43710035	Improving the analysis of NMR spectra tracking pH-induced conformational changes: removing artefacts of the electric field on the NMR chemical shift.
Q87839353	Improving the orientation-dependent statistical potential using a reference state
Q30327787	Improving the performance of Rosetta using multiple sequence alignment information and global measures of hydrophobic core formation.
Q37083941	Improving the prediction accuracy of residue solvent accessibility and real-value backbone torsion angles of proteins by guided-learning through a two-layer neural network.
Q30330078	Improving the prediction of protein secondary structure in three and eight classes using recurrent neural networks and profiles.
Q44817547	Improving the tolerance of a protein a analogue to repeated alkaline exposures using a bypass mutagenesis approach
Q33844352	Improving threading algorithms for remote homology modeling by combining fragment and template comparisons
Q28235593	In Memoriam: Frederic M. Richards (1925-2009)
Q79098378	In Silico
Q67797005	In memoriam--Cyrus Levinthal
Q47587723	In memoriam. Angel Ramírez Ortiz (1966-2008).
Q48474537	In memoriam: Charles Tanford(1921-2009).
Q49157447	In memoriam: Irving S. Sigal 1953-1988.
Q27649290	In meso crystal structure and docking simulations suggest an alternative proteoglycan binding site in the OpcA outer membrane adhesin
Q43170586	In pursuit of virtual lead optimization: pruning ensembles of receptor structures for increased efficiency and accuracy during docking
Q40419101	In pursuit of virtual lead optimization: the role of the receptor structure and ensembles in accurate docking
Q46296776	In silico analyses of substrate interactions with human serum paraoxonase 1.
Q33439048	In silico characterization of protein chimeras: relating sequence and function within the same fold.
Q90516587	In silico design and molecular basis for the selectivity of Olinone toward the first over the second bromodomain of BRD4
Q33302443	In silico local structure approach: a case study on outer membrane proteins
Q39037535	In silico modeling of pH‐optimum of protein–protein binding
Q51720267	In silico mutational studies of Hsp70 disclose sites with distinct functional attributes
Q53302216	In silico platform for predicting and initiating β-turns in a protein at desired locations.
Q84171308	In silico predictions of LH2 ring sizes from the crystal structure of a single subunit using molecular dynamics simulations
Q46778241	In silico structure-function analysis of E. cloacae nitroreductase
Q45138458	In silico study of the human rhodopsin and meta rhodopsin II/S-arrestin complexes: impact of single point mutations related to retina degenerative diseases.
Q54547905	In silico two-hybrid system for the selection of physically interacting protein pairs.
Q92309391	In vitro and in silico studies on membrane interactions of diverse Capsicum annuum flower γ-thionin peptides
Q47893467	In vitro and in vivo characterization of designed immunogens derived from the CD-helix of the stem of influenza hemagglutinin
Q54583935	In vivo association of protein fragments giving active AraC.
Q46194098	Inclusion of ionization states of ligands in affinity calculations
Q37565089	Inclusion of the orientational entropic effect and low-resolution experimental information for protein-protein docking in Critical Assessment of PRedicted Interactions (CAPRI).
Q51905246	Incorporating biochemical information and backbone flexibility in RosettaDock for CAPRI rounds 6-12.
Q86534498	Incorporating into a Cα Go model the effects of geometrical restriction on Cα atoms caused by side chain orientations
Q30359220	Incorporating replacement free energy of binding-site waters in molecular docking.
Q41768307	Incorporation of evolutionary information into Rosetta comparative modeling
Q51970520	Incorporation of flexibility into rigid-body docking: applications in rounds 3-5 of CAPRI.
Q45768018	Incorporation of microcrystals by growing protein and virus crystals
Q30332739	Increased detection of structural templates using alignments of designed sequences
Q57472390	Increased sequence hydrophobicity reduces conformational specificity: a mutational case study of the Arc repressor protein
Q42095915	Increasing protein stability by improving beta-turns
Q43665065	Increasing stability of antibody via antibody engineering: stability engineering on an anti-hVEGF.
Q33217621	Increasing the molecular contacts between maurotoxin and Kv1.2 channel augments ligand affinity.
Q28874041	Increasing the precision of comparative models with YASARA NOVA-a self-parameterizing force field
Q50545034	Indefinite noncooperative self‐association of chicken deoxy hemoglobin D
Q40249508	Indel-based targeting of essential proteins in human pathogens that have close host orthologue(s): discovery of selective inhibitors for Leishmania donovani elongation factor-1alpha
Q41134627	Induced conformational change in human IL-4 upon binding of a signal-neutralizing DARPin
Q42645383	Induced fit in liver X receptor beta: a molecular dynamics-based investigation
Q50771478	Induced refolding of a temperature denatured llama heavy-chain antibody fragment by its antigen
Q45922397	Induction of the tetracycline repressor: characterization by molecular-dynamics simulations.
Q44366842	Inferring a weighted elastic network from partial unfolding with coarse-grained simulations
Q40191495	Inferring ideal amino acid interaction forms from statistical protein contact potentials
Q31028667	Inferring protein interactions from experimental data by association probabilistic method
Q30884368	Inferring the microscopic surface energy of protein-protein interfaces from mutation data.
Q97557445	Influence of Electrostatic Forces on the Association Kinetics and Conformational Ensemble of an Intrinsically Disordered Protein
Q104474626	Influence of Sequence Length and Charged Residues on Swc5 Binding with Histone H2A-H2B
Q30361618	Influence of a heptad repeat stutter on the pH-dependent conformational behavior of the central coiled-coil from influenza hemagglutinin HA2
Q46449574	Influence of conservation on calculations of amino acid covariance in multiple sequence alignments
Q30372936	Influence of different assignment conditions on the determination of symmetric homodimeric structures with ARIA.
Q38361551	Influence of induced fit in the interaction of Bacillus subtilis trp RNA-binding attenuator protein and its RNA antiterminator target oligomer
Q54585320	Influence of kinetics of drug binding on EGFR signaling: A comparative study of three EGFR signaling pathway models
Q41470212	Influence of oligomerization on the dynamics of G-protein coupled receptors as assessed by normal mode analysis
Q34389407	Influence of oligomerization state on the structural properties of invasion plasmid antigen B from Shigella flexneri in the presence and absence of phospholipid membranes.
Q64923362	Influence of pressure on the low‐frequency vibrational modes of lysozyme and water: A complementary inelastic neutron scattering and molecular dynamics simulation study
Q52389860	Influence of protein flexibility on the redox potential of rubredoxin: energy minimization studies
Q30430527	Influence of protein structure databases on the predictive power of statistical pair potentials
Q49265475	Influence of rotational energy barriers to the conformational search of protein loops in molecular dynamics and ranking the conformations
Q44165213	Influence of solvent molecules on the stereochemical code of glycyl residues in proteins
Q30352413	Influence of the disulfide bond configuration on the dynamics of the spin label attached to cytochrome c.
Q80660489	Influence of the germline sequence on the thermodynamic stability and fibrillogenicity of human lambda 6 light chains
Q79252711	Influence of the protein matrix on intramolecular histidine ligation in ferric and ferrous hexacoordinate hemoglobins
Q30365841	Information and discrimination in pairwise contact potentials.
Q50726214	Information and redundancy in the burial folding code of globular proteins within a wide range of shapes and sizes
Q30371405	Information theory provides a comprehensive framework for the evaluation of protein structure predictions.
Q30383895	Information-theoretic analysis of the reference state in contact potentials used for protein structure prediction.
Q30331650	Information-theoretic dissection of pairwise contact potentials.
Q44886386	Information-theoretical entropy as a measure of sequence variability
Q50673825	Inhibition of Ribonuclease A by polyphenols present in green tea.
Q53175065	Inhibition of interdomain motion in g‐actin by the natural product latrunculin: A molecular dynamics study
Q57937295	Inhibition of protein-protein interactions: The discovery of druglike β-catenin inhibitors by combining virtual and biophysical screening
Q62994772	Inhibition of trypsin by cowpea thionin: Characterization, molecular modeling, and docking
Q53322022	Inhibition of α-synuclein aggregation by small heat shock proteins.
Q44125142	Inhibitor binding alters the directions of domain motions in HIV-1 reverse transcriptase
Q75348990	Inhomogeneous stability of bacteriorhodopsin in purple membrane against photobleaching at high temperature
Q45352137	Inositol phosphates compete with nucleic acids for binding to bovine leukemia virus matrix protein: Implications for deltaretroviral assembly
Q34361791	Insertion of peptide chains into lipid membranes: an off-lattice Monte Carlo dynamics model
Q51109313	Insight into the activity of SARS main protease: Molecular dynamics study of dimeric and monomeric form of enzyme
Q27652353	Insight into the antibacterial drug design and architectural mechanism of peptide recognition from the E. faecium peptide deformylase structure
Q79323943	Insight into the catalytic mechanism of arginine deiminase: functional studies on the crucial sites
Q52847435	Insight into the correlation between lag time and aggregation rate in the kinetics of protein aggregation
Q30362621	Insight into the early stages of thermal unfolding of peanut agglutinin by molecular dynamics simulations.
Q40255470	Insight into the remarkable affinity and selectivity of the aminobenzosuberone scaffold for the M1 aminopeptidases family based on structure analysis.
Q44601566	Insight into the stability of the hydrophobic binding proteins ofescherichia coli:Assessing the proteins for use as biosensors
Q27659155	Insight into the structure of the pUL89 C-terminal domain of the human cytomegalovirus terminase complex
Q27656119	Insight into the substrate length restriction of M32 carboxypeptidases: characterization of two distinct subfamilies
Q46668209	Insights from the energetics of water binding at the domain-ligand interface of the Src SH2 domain
Q27666117	Insights into Mycoplasma genitalium metabolism revealed by the structure of MG289, an extracytoplasmic thiamine binding lipoprotein
Q104695529	Insights into Specificity and Catalytic Mechanism of Amphotericin B/Nystatin Thioesterase
Q34416381	Insights into a highly conserved network of hydrogen bonds in the agonist binding site of nicotinic acetylcholine receptors: a structural and theoretical study
Q46814788	Insights into activation and RNA binding of trp RNA-binding attenuation protein (TRAP) through all-atom simulations
Q83319759	Insights into internal dynamics of 6-phosphogluconolactonase from Trypanosoma brucei studied by nuclear magnetic resonance and molecular dynamics
Q45993120	Insights into lid movements of Burkholderia cepacia lipase inferred from molecular dynamics simulations.
Q50858078	Insights into mechanism of pyrido[2,3-d]pyrimidines as DYRK1A inhibitors based on molecular dynamic simulations
Q58375365	Insights into nonspecific binding of homeodomains from a structure of MATα2 bound to DNA
Q30357462	Insights into protein structure and function from disorder-complexity space.
Q27703595	Insights into regioselective metabolism of mefenamic acid by cytochrome P450 BM3 mutants through crystallography, docking, molecular dynamics, and free energy calculations
Q47367614	Insights into the DNA cleavage mechanism of human LINE-1 retrotransposon endonuclease
Q27640184	Insights into the bile acid transportation system: the human ileal lipid-binding protein-cholyltaurine complex and its comparison with homologous structures
Q27654533	Insights into the catalytic mechanism of the Bcp family: functional and structural analysis of Bcp1 from Sulfolobus solfataricus
Q39038050	Insights into the interaction of high potency inhibitor IRC-083864 with phosphatase CDC25.
Q80626072	Insights into the interactions between HIV-1 integrase and human LEDGF/p75 by molecular dynamics simulation and free energy calculation
Q27621102	Insights into the mechanisms of catalysis and heterotropic regulation of Escherichia coli aspartate transcarbamoylase based upon a structure of the enzyme complexed with the bisubstrate analogue N-phosphonacetyl-L-aspartate at 2.1 A
Q27649854	Insights into the role of oligomeric state on the biological activities of crotoxin: crystal structure of a tetrameric phospholipase A2 formed by two isoforms of crotoxin B from Crotalus durissus terrificus venom
Q38859454	Insights into the transmembrane helix associations of kit ligand by molecular dynamics simulation and TOXCAT.
Q30428835	Insights into thermal resistance of proteins from the intrinsic stability of their α-helices
Q80020949	Insights into unbinding mechanisms upon two mutations investigated by molecular dynamics study of GSK3beta-axin complex: role of packing hydrophobic residues
Q31026877	Insights on HIV-1 Tat:P/CAF bromodomain molecular recognition from in vivo experiments and molecular dynamics simulations.
Q45342240	Insights on Na+ binding and conformational dynamics in multidrug and toxic compound extrusion transporter NorM
Q57278500	Insights on the acetylated NF-κB transcription factor complex with DNA from molecular dynamics simulations
Q91787001	Inspecting fluctuation and coordination around chromophore inside green fluorescent protein from water to nonpolar solvent
Q71763596	Insulin and epidermal growth factor receptors contain the cysteine repeat motif found in the tumor necrosis factor receptor
Q52053619	Integrated graphical analysis of protein sequence features predicted from sequence composition
Q51639697	Integrated prediction of the effect of mutations on multiple protein characteristics.
Q51626110	Integrating statistical pair potentials into protein complex prediction
Q34975505	Integrating the intrinsic conformational preferences of noncoded α-amino acids modified at the peptide bond into the noncoded amino acids database
Q30379180	Integration of QUARK and I-TASSER for Ab Initio Protein Structure Prediction in CASP11.
Q91349229	Integrative modeling of protein-protein interactions with pyDock for the new docking challenges
Q68151698	Integrity of refolded and reoxidized gelatin-binding fragments of fibronectin
Q44784442	Inter-residue and solvent-residue interactions in proteins: a statistical study on experimental structures
Q30399514	InterPred: A pipeline to identify and model protein-protein interactions.
Q53336814	Interacting processes in protein coagulation
Q30380846	Interaction between bound water molecules and local protein structures: A statistical analysis of the hydrogen bond structures around bound water molecules.
Q46917665	Interaction between mammalian glyceraldehyde-3-phosphate dehydrogenase and L-lactate dehydrogenase from heart and muscle
Q81383339	Interaction cutoff effect on ruggedness of protein-protein energy landscape
Q79554810	Interaction geometry involving planar groups in protein-protein interfaces
Q81054160	Interaction interfaces of protein domains are not topologically equivalent across families within superfamilies: Implications for metabolic and signaling pathways
Q50730119	Interaction of (-)-epigallocatechin-3-gallate with human serum albumin: fluorescence, fourier transform infrared, circular dichroism, and docking studies
Q38359685	Interaction of E. coli outer-membrane protein A with sugars on the receptors of the brain microvascular endothelial cells
Q28214346	Interaction of Hsp90 with 20S proteasome: thermodynamic and kinetic characterization
Q28183468	Interaction of agitoxin2, charybdotoxin, and iberiotoxin with potassium channels: selectivity between voltage-gated and Maxi-K channels
Q77133311	Interaction of explicit solvent with hydrophobic/philic/charged residues of a protein: residue character vs. conformational context
Q32061110	Interaction of human SRY protein with DNA: A molecular dynamics study
Q40259593	Interaction of malaria parasite-inhibitory antibodies with the merozoite surface protein MSP1(19) by computational docking
Q53337296	Interaction of metal chelators with different molecular forms of acetylcholinesterase and its significance in Alzheimer's disease treatment
Q46834876	Interaction of peptide boronic acids with elastase: circular dichroism studies
Q52243202	Interaction of transmembrane helices by a knobs-into-holes packing characteristic of soluble coiled coils
Q74363284	Interaction potentials for protein folding
Q54701079	Interaction stabilizing tertiary structure of bacteriorhodopsin studied by denaturation experiments.
Q35948844	Interactions between relay helix and Src homology 1 (SH1) domain helix drive the converter domain rotation during the recovery stroke of myosin II
Q27652877	Interactions between the archaeal transcription repressor FL11 and its coregulators lysine and arginine
Q53579152	Interactions between the toxin Kid of the bacterial parD system and the antitoxins Kis and MazE.
Q27633855	Interactions of Streptomyces griseus aminopeptidase with amino acid reaction products and their implications toward a catalytic mechanism
Q37286930	Interactions of different inhibitors with active-site aspartyl residues of HIV-1 protease and possible relevance to pepsin
Q28263652	Interactions of macromolecules with salt ions: an electrostatic theory for the Hofmeister effect
Q33242650	Interactions of the C2 domain of human factor V with a model membrane
Q46823198	Interdomain cooperativity of calmodulin bound to melittin preferentially increases calcium affinity of sites I and II.
Q53599719	Interdomain mobility in di-ubiquitin revealed by NMR.
Q92513897	Interfacial amino acids support Spa47 oligomerization and shigella type three secretion system activation
Q43947468	Interhelical hydrogen bonds and spatial motifs in membrane proteins: polar clamps and serine zippers
Q85910653	Intermolecular disulfide bond formation promotes immunoglobulin aggregation: investigation by fluorescence correlation spectroscopy
Q70248265	Internal motion of a tryptophan residue in Streptomyces subtilisin inhibitor: deuterium nuclear magnetic resonance in solution
Q35093508	Internal organization of large protein families: relationship between the sequence, structure, and function-based clustering
Q28822365	Interolog interfaces in protein-protein docking
Q35687847	Interpeptide interactions induce helix to strand structural transition in Abeta peptides
Q51412572	Interplay between binding affinity and kinetics in protein-protein interactions
Q46586541	Interplay between structural rigidity and electrostatic interactions in the ligand binding domain of GluR2.
Q30431832	Interplay of I‐TASSER and QUARK for template‐based and ab initio protein structure prediction in CASP10
Q90304563	Interplay of cysteine exposure and global protein dynamics in small-molecule recognition by a regulator of G-protein signaling protein
Q73205383	Interresidue interactions in protein classes
Q27766078	Intersubunit hydrogen bond acts as a global molecular switch in Escherichia coli aspartate transcarbamoylase
Q27680314	Intramolecular isopeptide but not internal thioester bonds confer proteolytic and significant thermal stability to theS. pyogenespilus adhesin Spy0125
Q35153112	Intramolecular localization of epitopes within an oligomeric protein by immunoelectron microscopy and image processing
Q89311088	Intrinsic disorder accelerates dissociation rather than association
Q80353265	Intrinsic disorder in yeast transcriptional regulatory network
Q52664522	Intrinsic disorder is a key characteristic in partners that bind 14-3-3 proteins.
Q51896014	Intrinsic disorder of Drosophila melanogaster hormone receptor 38 N-terminal domain.
Q53219534	Intrinsic disorder of human Yin Yang 1 protein
Q57137427	Intrinsic pKas of ionizable residues in proteins: an explicit solvent calculation for lysozyme
Q52364819	Intrinsic secondary structure propensities of the amino acids, using statistical phi-psi matrices: comparison with experimental scales
Q28910370	Intrinsic structural disorder and sequence features of the cell cycle inhibitor p57Kip2
Q45340609	Intrinsic structural disorder of mouse proNGF.
Q81507965	Intrinsic unstructuredness and abundance of PEST motifs in eukaryotic proteomes
Q39114601	Intrinsic α helix propensities compact hydrodynamic radii in intrinsically disordered proteins
Q46899115	Intrinsically disordered protein from a pathogenic mesophile Mycobacterium tuberculosis adopts structured conformation at high temperature
Q39335014	Intrinsically disordered regions in autophagy proteins
Q65000375	Intrinsically unstructured N-terminal domain of bZIP transcription factor HY5.
Q90393811	Introducing "best single template" models as reference baseline for the Continuous Automated Model Evaluation (CAMEO)
Q44862616	Introducing folding stability into the score function for computational design of RNA-binding peptides boosts the probability of success
Q27667224	Introduction of a disulfide bond leads to stabilization and crystallization of a ricin immunogen
Q46166584	Intron/exon structure of the human gene for the muscle isozyme of glycogen phosphorylase
Q44990288	Intuitive, but not simple: including explicit water molecules in protein-protein docking simulations improves model quality.
Q27643968	Invariance of the zinc finger module: a comparison of the free structure with those in nucleic-acid complexes
Q59210376	Invariant Ser211 is involved in the catalysis of PD-L4, type I RIP from Phytolacca dioica leaves
Q47554413	Investigating Energy-Based Pool Structure Selection in the Structure Ensemble Modeling with Experimental Distance Constraints: The Example from a Multi-Domain Protein Pub1.
Q77386266	Investigating a back door mechanism of actin phosphate release by steered molecular dynamics
Q96585349	Investigating dual Ca2+ modulation of the ryanodine receptor 1 by molecular dynamics simulation
Q91076218	Investigating role of conformational changes of microtubule in regulating its binding affinity to kinesin by all-atom molecular dynamics simulation
Q27653170	Investigating the binding of beta-1,4-galactan to Bacillus licheniformis beta-1,4-galactanase by crystallography and computational modeling
Q47547727	Investigating the effect of key mutations on the conformational dynamics of Toll-like receptor dimers through molecular dynamics simulations and protein structure networks
Q38683377	Investigating the inter-subunit/subdomain interactions and motions relevant to disease mutations in the N-terminal domain of ryanodine receptors by molecular dynamics simulation
Q42409589	Investigating the linkage between disease-causing amino acid variants and their effect on protein stability and binding
Q30456752	Investigating the mutation resistance of nonnucleoside inhibitors of HIV-RT using multiple microsecond atomistic simulations
Q91163110	Investigating the stability of dengue virus envelope protein dimer using well-tempered metadynamics simulations
Q41596452	Investigating the structural dynamics of the PIEZO1 channel activation and inactivation by coarse-grained modeling
Q38299971	Investigating the structural stability of the Tup1-interaction domain of Ssn6: evidence for a conformational change on the complex.
Q30332014	Investigating the ultrastructure of fibrous long spacing collagen by parallel atomic force and transmission electron microscopy.
Q44855337	Investigation of glucose binding sites on insulin
Q47367719	Investigation of molecular size of transcription factor TFIIE in solution.
Q52340739	Investigation of the folding pathway of the TEM-1 beta-lactamase
Q38324015	Investigation of the function of mutated cellulose-binding domains of Trichoderma reesei cellobiohydrolase I
Q57843045	Investigation of the functional interplay between the primary site and the subsite of RNase T1: Kinetic analysis of single and multiple mutants for modified substrates
Q44544336	Investigation of the induced-fit mechanism and catalytic activity of the human cytomegalovirus protease homodimer via molecular dynamics simulations
Q30375050	Investigation of the molecular similarity in closely related protein systems: The PrP case study.
Q57831465	Investigation of transcription factor Ndt80 affinity differences for wild type and mutant DNA: A molecular dynamics study
Q46938187	Involvement of disulfide bonds and histidine 172 in a unique beta-sheet to alpha-helix transition of alpha 1-acid glycoprotein at the biomembrane interface
Q41652149	In‐cell protein NMR and protein leakage
Q46982745	Ion exclusion mechanism in aquaporin at an atomistic level
Q52378782	Ion pair formation involving methylated lysine side chains: a theoretical study
Q51649750	Ion pair formation of phosphorylated amino acids and lysine and arginine side chains: a theoretical study
Q63214351	Ion pairs and their role in modulating stability of cold- and warm-active uracil DNA glycosylase
Q68697910	Ion pairs in alpha helices
Q44242207	Ion permeation through the gramicidin channel: atomically detailed modeling by the Stochastic Difference Equation
Q45039438	Ion transit pathways and gating in ClC chloride channels
Q73864352	Ion-induced conformational and stability changes in Nereis sarcoplasmic calcium binding protein: evidence that the APO state is a molten globule
Q58413098	Ionic network at the C-terminus of the ?-glycosidase from the hyperthermophilic archaeonSulfolobus solfataricus: Functional role in the quaternary structure thermal stabilization
Q35229574	Ionic strength dependence of F‐actin and glycolytic enzyme associations: A Brownian dynamics simulations approach
Q57904261	Ionization Behavior of Acidic Residues in Calbindin D9k
Q30322874	Ionization behavior of acidic residues in calbindin D(9k).
Q47596290	Irreversible formation of intermediate BSA oligomers requires and induces conformational changes
Q43238277	Is Asp-His-Ser/Thr-Trp tetrad hydrogen-bond network important to WD40-repeat proteins: a statistical and theoretical study
Q35894622	Is allostery an intrinsic property of all dynamic proteins?
Q73134818	Is cyanate a carbonic anhydrase substrate?
Q44855342	Is histoaspartic protease a serine protease with a pepsin-like fold?
Q52066244	Is it a paradox or misinterpretation?
Q53214167	Is the binding of beta-amyloid protein to antichymotrypsin in Alzheimer plaques mediated by a beta-strand insertion?
Q27685370	Is the bovine lysosomal phospholipase B-like protein an amidase?
Q74093201	Is the molten globule a third thermodynamic state of protein? The example of α-lactalbumin
Q82451701	Is the prediction of pKavalues by constant‐pH molecular dynamics being hindered by inherited problems?
Q44745626	Is there a weak H-bond --> LBHB transition on tetrahedral complex formation in serine proteases?
Q46650397	Is there nascent structure in the intrinsically disordered region of troponin I?
Q52696012	Isoform-specific variation in the intrinsic disorder of the ecdysteroid receptor N-terminal domain
Q45964612	Isoform-specific variation in the intrinsic disorder of troponin I.
Q45141440	Isolation and analysis of arc repressor mutants: evidence for an unusual mechanism of DNA binding
Q46488478	Isolation and characterization of native human renin derived from Chinese hamster ovary cells
Q27666733	Isolation, kinetic analysis, and structural characterization of an antibody targeting the Bacillus anthracis major spore surface protein BclA
Q72589792	Isotope effects in peptide group hydrogen exchange
Q126290317	Issue Information ‐ Forthcoming
Q45159481	Issues in high-throughput comparative modelling: a case study using the ubiquitin E2 conjugating enzymes
Q30496342	Iterative cluster-NMA: A tool for generating conformational transitions in proteins
Q51550360	KFC2: A knowledge‐based hot spot prediction method based on interface solvation, atomic density, and plasticity features
Q28646973	Key challenges for the creation and maintenance of specialist protein resources
Q41669208	Key mutations stabilize antigen-binding conformation during affinity maturation of a broadly neutralizing influenza antibody lineage
Q33180488	Key residues approach to the definition of protein families and analysis of sparse family signatures
Q105099846	Key residues approach to the definition of protein families and analysis of sparse family signatures
Q44195807	Kinase inhibitors and the case for CH...O hydrogen bonds in protein-ligand binding
Q36218605	Kinesin tail domains are intrinsically disordered.
Q81230771	Kinetic analysis of molecular dynamics simulations reveals changes in the denatured state and switch of folding pathways upon single-point mutation of a beta-sheet miniprotein
Q62666988	Kinetic analysis of the interaction between the QutA and QutR transcription-regulating proteins
Q33479643	Kinetic and binding effects in peptide substrate selectivity of matrix metalloproteinase-2: Molecular dynamics and QM/MM calculations
Q46750678	Kinetic and crystallographic studies of glucopyranose spirohydantoin and glucopyranosylamine analogs inhibitors of glycogen phosphorylase.
Q57752568	Kinetic and structural properties of inorganic pyrophosphatase from the pathogenic bacterium Helicobacter pylori
Q27648882	Kinetic and structural properties of triosephosphate isomerase from Helicobacter pylori
Q54773800	Kinetic characterization of early intermediates in the folding of E. coli tryptophan-synthase beta 2 subunit.
Q52133639	Kinetic characterization of the interaction of the Z-fragment of protein A with mouse-IgG3 in a volume in chemical space
Q30010189	Kinetic consequences of native state optimization of surface-exposed electrostatic interactions in the Fyn SH3 domain
Q70980712	Kinetic folding and unfolding of staphylococcal nuclease and its six mutants studied by stopped-flow circular dichroism
Q73883517	Kinetic nonoptimality and vibrational stability of proteins
Q46105819	Kinetic steps for alpha-helix formation
Q72200787	Kinetic study on myoglobin refolding monitored by five optical probe stopped-flow methods
Q30157902	Kinetically driven refolding of the hyperstable EBNA1 origin DNA-binding dimeric beta-barrel domain into amyloid-like spherical oligomers
Q77669697	Kinetics and interaction studies between cytochrome c3 and Fe-only hydrogenase from Desulfovibrio vulgaris Hildenborough
Q46068436	Kinetics and thermodynamics of gas diffusion in a NiFe hydrogenase
Q44379452	Kinetics of cytochrome C folding: atomically detailed simulations
Q45039432	Kinetics of folding and unfolding of goat alpha-lactalbumin
Q89915402	Kinetics of pH-dependent interactions between PD-1 and PD-L1 immune checkpoint proteins from molecular dynamics
Q87726705	Kinetics of protein fibrillation controlled by fibril elongation
Q38337597	Kinetics, in silico docking, molecular dynamics, and MM‐GBSA binding studies on prototype indirubins, KT5720, and staurosporine as phosphorylase kinase ATP‐binding site inhibitors: The role of water molecules examined
Q30322116	Knowledge-based interaction potentials for proteins.
Q73427996	Knowledge-based modeling of a bacterial dichloromethane dehalogenase
Q59312602	Knowledge-based modeling of theD-lactate dehydrogenase three-dimensional structure
Q29547838	Knowledge-based protein secondary structure assignment
Q40377577	Knowledge-based voting algorithm for automated protein functional annotation
Q52340706	LINUS: a hierarchic procedure to predict the fold of a protein
Q33863846	LabCaS: labeling calpain substrate cleavage sites from amino acid sequence using conditional random fields
Q27635351	Lactoferrin-melanin interaction and its possible implications in melanin polymerization: crystal structure of the complex formed between mare lactoferrin and melanin monomers at 2.7-A resolution
Q52019786	Large contact surface interactions between proteins detected by time series analysis methods: case study on C-phycocyanins
Q73025524	Large contributions of coupled protonation equilibria to the observed enthalpy and heat capacity changes for ssDNA binding to Escherichia coli SSB protein
Q57091182	Large differences are observed between the crystal and solution quaternary structures of allosteric aspartate transcarbamylase in the R state
Q51602853	Large loop conformation sampling using the activation relaxation technique, ART-nouveau method
Q41308079	Large oligomeric complex structures can be computationally assembled by efficiently combining docked interfaces
Q48127175	Large scale ab initio modelling of structurally uncharacterized antimicrobial peptides reveals known and novel folds
Q51899750	Large scale analysis of protein-binding cavities using self-organizing maps and wavelet-based surface patches to describe functional properties, selectivity discrimination, and putative cross-reactivity
Q38509250	Large-scale analysis of secondary structure changes in proteins suggests a role for disorder-to-order transitions in nucleotide binding proteins
Q50936482	Large-scale analysis of the dynamics of enzymes
Q45944217	Large-scale automated function prediction of protein sequences and an experimental case study validation on PTEN transcript variants.
Q81433368	Large-scale characteristics of the energy landscape in protein-protein interactions
Q46972510	Large-scale comparison of protein sequence alignment algorithms with structure alignments
Q46244966	Large-scale prediction of disulphide bridges using kernel methods, two-dimensional recursive neural networks, and weighted graph matching
Q57444201	Large-scale prediction of function shift in protein families with a focus on enzymatic function
Q44491602	Large-scale prediction of protein geometry and stability changes for arbitrary single point mutations
Q58323028	Large-scale purification and preliminary X-ray diffraction studies of human aspartylglucosaminidase
Q43525502	Large-scale survey for potentially targetable indels in bacterial and protozoan proteins
Q30393805	Large‐scale comparison of protein essential dynamics from molecular dynamics simulations and coarse‐grained normal mode analyses
Q81210075	Lattice models, packing density, and Boltzmann-like distribution of cavities in proteins
Q30328050	Lattice protein folding with two and four-body statistical potentials.
Q44932031	Lattice simulations of cotranslational folding of single domain proteins
Q30369016	Lattices for ab initio protein structure prediction.
Q91189840	Learning a functional grammar of protein domains using natural language word embedding techniques
Q30419136	Learning about protein folding via potential functions
Q43711450	Learning about protein hydrogen bonding by minimizing contrastive divergence.
Q52142055	Learning effective amino acid interactions through iterative stochastic techniques.
Q51609601	Learning generative models for protein fold families
Q46448828	Lecithin:cholesterol acyltransferase activation by synthetic amphipathic peptides
Q64911673	Left-handed polyproline II helix formation is (very) locally driven.
Q40909294	Length distribution of CDRH3 in antibodies
Q39324146	Lessons from (co-)evolution in the docking of proteins and peptides for CAPRI Rounds 28-35.
Q40823351	Lethal mutations in the major homology region and their suppressors act by modulating the dimerization of the rous sarcoma virus capsid protein C‐terminal domain
Q52610867	Leukocyte integrin αLβ2 transmembrane association dynamics revealed by coarse-grained molecular dynamics simulations.
Q33290508	Library of local descriptors models the core of proteins accurately
Q34805228	Ligand binding and dynamics of the monomeric epidermal growth factor receptor ectodomain
Q91793230	Ligand nanovectorization using graphene to target cellular death receptors of cancer cell
Q30489539	Ligand preference and orientation in b- and c-type heme-binding proteins
Q52214239	Ligand solvation in molecular docking
Q44195805	Ligand specificity and ligand-induced conformational change in gal repressor
Q44685771	Ligand unbinding from the estrogen receptor: a computational study of pathways and ligand specificity
Q46671657	Ligand-based protein alignment and isozyme specificity of glutathione S-transferase inhibitors
Q56877641	Ligand-induced dynamical regulation of NO conversion in Mycobacterium tuberculosis truncated hemoglobin-N
Q42660634	Ligand-induced fit in mycobacterial MabA: the sequence-specific C-terminus locks the conformational change
Q52890990	Ligand-induced formation of transient dimers of mammalian 12/15-lipoxygenase: a key to allosteric behavior of this class of enzymes?
Q104618319	Ligand-induced transition in conformations of vicinal cysteine disulfides in proteins
Q96290019	Ligand-protein interactions in lysozyme investigated through a dual-resolution model
Q43558049	Ligand-protein inverse docking and its potential use in the computer search of protein targets of a small molecule
Q79223169	Ligand-supported homology modeling of the human angiotensin II type 1 (AT(1)) receptor: insights into the molecular determinants of telmisartan binding
Q81481787	Limited validity of group additivity for the folding energetics of the peptide group
Q41104358	Limits on alpha-helix prediction with neural network models
Q34050401	Linear extrapolation method of analyzing solvent denaturation curves
Q74615900	Linear programming optimization and a double statistical filter for protein threading protocols
Q45070176	Linear response theory: an alternative to PB and GB methods for the analysis of molecular dynamics trajectories?
Q33232121	Linker chains of the gigantic hemoglobin of the earthworm Lumbricus terrestris: primary structures of linkers L2, L3, and L4 and analysis of the connectivity of the disulfide bonds in linker L1.
Q36075396	Linking tumor cell cytotoxicity to mechanism of drug action: an integrated analysis of gene expression, small-molecule screening and structural databases
Q45852371	Lipid A from lipopolysaccharide recognition: structure, dynamics and cooperativity by molecular dynamics simulations.
Q46814799	Lipid membrane templates the ordering and induces the fibrillogenesis of Alzheimer's disease amyloid-beta peptide
Q30363926	Lipid nanotechnologies for structural studies of membrane-associated proteins
Q30850744	Lipid-associated aggregate formation of superoxide dismutase-1 is initiated by membrane-targeting loops
Q46534332	Lipophobicity and the residue environments of the transmembrane alpha-helical bundle
Q57015034	Lipoprotein lipase: A bioinformatics criterion for assessment of mutations as a risk factor for cardiovascular disease
Q27642889	Lipoxygenase interactions with natural flavonoid, quercetin, reveal a complex with protocatechuic acid in its X-ray structure at 2.1 A resolution
Q30329580	LiveBench-2: large-scale automated evaluation of protein structure prediction servers.
Q30336308	LiveBench-6: large-scale automated evaluation of protein structure prediction servers.
Q56877450	Lobster enolase crystallized by serendipity
Q30373443	Local descriptors of protein structure: a systematic analysis of the sequence-structure relationship in proteins using short- and long-range interactions
Q30331169	Local energy landscape flattening: parallel hyperbolic Monte Carlo sampling of protein folding.
Q83341005	Local feature analysis: a statistical theory for reproducible essential dynamics of large macromolecules
Q30428832	Local interactions and the optimization of protein folding
Q51903851	Local interactions in protein folding determined through an inverse folding model
Q58042910	Local interactions in protein folding determined through an inverse folding model
Q53017556	Local motions in a benchmark of allosteric proteins
Q52330897	Local moves: an efficient algorithm for simulation of protein folding
Q44322001	Local protein unfolding and pathogenesis of polyglutamine-expansion diseases
Q87167117	Local sequence of protein β-strands influences twist and bend angles
Q47694030	Local-scale repetitiveness in amino acid use in eukaryote protein sequences: a genomic factor in protein evolution
Q52392511	Localization of hydrogen-bonds within modules in barnase
Q27628951	Localization of the C-terminus of rat glutathione S-transferase A1-1: crystal structure of mutants W21F and W21F/F220Y
Q46080127	Locally defined protein phylogenetic profiles reveal previously missed protein interactions and functional relationships
Q27621096	Locating interaction sites on proteins: the crystal structure of thermolysin soaked in 2% to 100% isopropanol
Q30358933	Locating missing water molecules in protein cavities by the three-dimensional reference interaction site model theory of molecular solvation.
Q61836416	Locating the active sites of enzymes using mechanical properties
Q47867085	Locating the stabilizing residues in (alpha/beta)8 barrel proteins based on hydrophobicity, long-range interactions, and sequence conservation
Q35574706	Long dynamics simulations of proteins using atomistic force fields and a continuum representation of solvent effects: calculation of structural and dynamic properties
Q51934735	Long loop prediction using the protein local optimization program
Q47632010	Long timestep dynamics of peptides by the dynamics driver approach
Q78627282	Long- and short-range interactions in native protein structures are consistent/minimally frustrated in sequence space
Q35791084	Longer simulations sample larger subspaces of conformations while maintaining robust mechanisms of motion
Q41875634	Loop modeling: Sampling, filtering, and scoring
Q49084735	Loop prediction for a GPCR homology model: Algorithms and results
Q80380695	Loop-closure events during protein folding: rationalizing the shape of Phi-value distributions
Q48406515	Loss of intramolecular electrostatic interactions and limited conformational ensemble may promote self-association of cis-tau peptide
Q73427985	Loss of translational entropy in binding, folding, and catalysis
Q44713138	Loss of translational entropy in molecular associations
Q52680163	Low pressure-induced secondary structure transitions of regenerated silk fibroin in its wet film studied by time-resolved infrared spectroscopy.
Q30158062	Low-throughput model design of protein folding inhibitors.
Q43027594	Lower kinetic limit to protein thermal stability: a proposal regarding protein stability in vivo and its relation with misfolding diseases
Q46668369	Lysine carboxylation in proteins: OXA-10 beta-lactamase
Q104474642	Lysine-Arginine Advanced Glycation End-Product Cross-links and the Effect on Collagen Structure: A Molecular Dynamics Study
Q70397716	Lysine/fibrin binding sites of kringles modeled after the structure of kringle 1 of prothrombin
Q90516630	Lysosomal acid lipase does not have a propeptide and should not be considered being a proprotein
Q74054770	M13 endopeptidases: New conserved motifs correlated with structure, and simultaneous phylogenetic occurrence of PHEX and the bony fish
Q97554798	M42 aminopeptidase catalytic site: the structural and functional role of a strictly conserved aspartate residue
Q47844501	MAAP: malarial adhesins and adhesin-like proteins predictor
Q28286817	MADAMM: a multistaged docking with an automated molecular modeling protocol
Q53028808	MALIDUP: a database of manually constructed structure alignments for duplicated domain pairs
Q51532804	MCCE analysis of the pKas of introduced buried acids and bases in staphylococcal nuclease
Q52082500	MCSS functionality maps for a flexible protein
Q99203054	MD Simulation Reveals Differential Binding of Cm(III) and Th(IV) with Serum Transferrin at Acidic pH
Q67584048	MD simulation of subtilisin BPN' in a crystal environment
Q92954714	MD simulations reveal alternate conformations of the oxyanion hole in the Zika virus NS2B/NS3 protease
Q34188650	MDockPP: A hierarchical approach for protein-protein docking and its application to CAPRI rounds 15-19
Q52033384	MIAX: a new paradigm for modeling biomacromolecular interactions and complex formation in condensed phases
Q43995264	MINOES: a new approach to select a representative ensemble of structures in NMR studies of (partially) unfolded states. Application to Delta25-PYP.
Q60218560	MM/PBSA analysis of molecular dynamics simulations of bovine β-lactoglobulin: Free energy gradients in conformational transitions?
Q30968423	MOLE: a data management application based on a protein production data model
Q30352079	MOTOR: model assisted software for NMR structure determination.
Q30372373	MQAPsingle: A quasi single-model approach for estimation of the quality of individual protein structure models.
Q80829064	MSDsite: a database search and retrieval system for the analysis and viewing of bound ligands and active sites
Q50421442	MUFOLD-SS: New deep inception-inside-inception networks for protein secondary structure prediction.
Q30408138	MUFOLD-WQA: A new selective consensus method for quality assessment in protein structure prediction
Q30382728	MUFOLD: A new solution for protein 3D structure prediction
Q31113169	MULTIPROSPECTOR: an algorithm for the prediction of protein-protein interactions by multimeric threading
Q39775057	MUPRED: a tool for bridging the gap between template based methods and sequence profile based methods for protein secondary structure prediction
Q51190031	MUSTANG: a multiple structural alignment algorithm
Q24646301	MUSTER: Improving protein sequence profile-profile alignments by using multiple sources of structure information
Q101054538	Machine Learning-based Prediction of Enzyme Substrate Scope: Application to Bacterial Nitrilases
Q90650346	Machine learning techniques for protein function prediction
Q78010849	Macromolecular impurities and disorder in protein crystals
Q38312613	Magnetic resonance studies of the binding of oligonucleotide substrates to mutants of staphylococcal nuclease
Q34434237	Main-chain conformational tendencies of amino acids
Q31913216	Major differences in stability and dimerization properties of two chimeric mutants of human stefins
Q60214177	Major differences in stability and dimerization properties of two chimeric mutants of human stefins
Q52223877	Major structural determinants of transmembrane proteins identified by principal component analysis
Q77751667	Major subdomain rearrangement in HIV-1 reverse transcriptase simulated by molecular dynamics
Q27636869	Major venom allergen of yellow jackets, Ves v 5: structural characterization of a pathogenesis-related protein superfamily
Q34351595	Making optimal use of empirical energy functions: force-field parameterization in crystal space
Q31018502	Managing and mining protein crystallization data.
Q30374170	Manual classification strategies in the ECOD database.
Q57970638	Many residues in cytochromec populate alternative states under equilibrium conditions
Q38290276	Mapping alpha-helical induced folding within the intrinsically disordered C-terminal domain of the measles virus nucleoprotein by site-directed spin-labeling EPR spectroscopy
Q45503208	Mapping disease-related missense mutations in the immunoglobulin-like fold domain of lamin A/C reveals novel genotype-phenotype associations for laminopathies
Q34420724	Mapping mouse IL-13 binding regions using structure modeling, molecular docking, and high-density peptide microarray analysis
Q41946244	Mapping of ligand-binding cavities in proteins
Q29039687	Mapping pathways of allosteric communication in GroEL by analysis of correlated mutations
Q46111888	Mapping the accessibility of the disulfide crosslink network in the wool fiber cortex.
Q32083062	Mapping the active site of factor Xa by selective inhibitors: An NMR and MD study
Q67255662	Mapping the enzymatic active site of Pseudomonas aeruginosa exotoxin A
Q46127492	Mapping the intramolecular signal transduction of G-protein coupled receptors
Q44998316	Markovian Backbone Negentropies: Molecular descriptors for protein research. I. Predicting protein stability in Arc repressor mutants
Q31956679	Mass spectrometric identification and microcharacterization of proteins from electrophoretic gels: strategies and applications
Q31956695	Mass spectrometric mapping of ion channel proteins (porins) and identification of their supramolecular membrane assembly
Q34521360	Mass spectrometrical verification of stomatin-like protein 2 (SLP-2) primary structure
Q33289183	Mass spectrometry analysis of HIV-1 Vif reveals an increase in ordered structure upon oligomerization in regions necessary for viral infectivity
Q33221094	Mass spectrometry identification of NASP binding partners in HeLa cells
Q46106488	Massive conformation change in the prion protein: Using dual-basin structure-based models to find misfolding pathways
Q30379161	Massive integration of diverse protein quality assessment methods to improve template based modeling in CASP11.
Q46657761	Mean field analysis of FKBP12 complexes with FK506 and rapamycin: Implications for a role of crystallographic water molecules in molecular recognition and specificity
Q74177433	Measured and calculated effects of mutations in bacteriophage T4 lysozyme on interactions in solution
Q36871049	Measurement of water–amide proton exchange rates in the denatured state of staphylococcal nuclease by a magnetization transfer technique
Q30343829	Measurements of protein sequence-structure correlations.
Q44365446	Measures for the assessment of fuzzy predictions of protein secondary structure
Q57444431	Measures of threading specificity and accuracy
Q74252589	Measures of threading specificity and accuracy
Q39472349	Measuring the successes and deficiencies of constant pH molecular dynamics: a blind prediction study
Q30176556	Mechanical property of a TIM-barrel protein
Q37163199	Mechanical stability and differentially conserved physical-chemical properties of titin Ig-domains
Q83782512	Mechanical stability of multidomain proteins and novel mechanical clamps
Q83003864	Mechanical unfolding pathway and origin of mechanical stability of proteins of ubiquitin family: an investigation by steered molecular dynamics simulation
Q36823266	Mechanism and rate constants of the Cdc42 GTPase binding with intrinsically disordered effectors
Q27652354	Mechanism for multiple-substrates recognition of alpha-aminoadipate aminotransferase from Thermus thermophilus
Q34266155	Mechanism for the alpha-helix to beta-hairpin transition
Q89309727	Mechanism for verification of mismatched and homoduplex DNAs by nucleotides-bound MutS analyzed by molecular dynamics simulations
Q57206145	Mechanism of NAD(P)H:Quinone reductase: Ab initio studies of reduced flavin
Q43599714	Mechanism of NAD(P)H:quinone reductase: Ab initio studies of reduced flavin
Q30387043	Mechanism of allosteric propagation across a β-sheet structure investigated by molecular dynamics simulations.
Q33393750	Mechanism of formation of the C-terminal beta-hairpin of the B3 domain of the immunoglobulin binding protein G from Streptococcus. I. Importance of hydrophobic interactions in stabilization of beta-hairpin structure
Q42133852	Mechanism of formation of the C-terminal beta-hairpin of the B3 domain of the immunoglobulin binding protein G from Streptococcus. II. Interplay of local backbone conformational dynamics and long-range hydrophobic interactions in hairpin formation
Q42121452	Mechanism of formation of the C-terminal beta-hairpin of the B3 domain of the immunoglobulin binding protein G from Streptococcus. III. Dynamics of long-range hydrophobic interactions
Q80660538	Mechanism of induced folding: Both folding before binding and binding before folding can be realized in staphylococcal nuclease mutants
Q46794953	Mechanism of inhibition of wt-dihydrofolate reductase from E. coli by tea epigallocatechin-gallate
Q30168709	Mechanism of protein folding
Q68085499	Mechanism of protein folding: I. General considerations and refolding of myoglobin
Q83677152	Mechanism of reactant and product dissociation from the anthrax edema factor: a locally enhanced sampling and steered molecular dynamics study
Q78010867	Mechanism of substrate dephosphorylation in low Mr protein tyrosine phosphatase
Q51553044	Mechanisms for allosteric activation of protease DegS by ligand binding and oligomerization as revealed from molecular dynamics simulations
Q79342159	Mechanisms of guanosine triphosphate hydrolysis by Ras and Ras-GAP proteins as rationalized by ab initio QM/MM simulations
Q41668610	Mechanisms of signaling and related enzymes
Q79737563	Mechanistic events underlying odorant binding protein chemoreception
Q52612340	Mechanistic insight of photo-induced aggregation of chicken egg white lysozyme: the interplay between hydrophobic interactions and formation of intermolecular disulfide bonds
Q45846360	Mechanistic insights into Pin1 peptidyl-prolyl cis-trans isomerization from umbrella sampling simulations
Q33300264	Mechanistic insights into the inhibition of prostate specific antigen by beta-lactam class compounds
Q84248142	Mechanistic role of NS4A and substrate in the activation of HCV NS3 protease
Q41143699	Mechanistic studies of the apical sodium-dependent bile acid transporter
Q44817534	Melittin as model system for probing interactions between proteins and cyclodextrins
Q24603721	Membrane insertion of the FYVE domain is modulated by pH
Q80867947	Membrane-bound structure and energetics of alpha-synuclein
Q51853796	Merging chemical and biological space: Structural mapping of enzyme binding pocket space
Q45397837	Metal binding sites of human H‐chain ferritin and iron transport mechanism to the ferroxidase sites: A molecular dynamics simulation study
Q54686771	Metal ion stabilization of the conformation of a recombinant 19‐kDa catalytic fragment of human fibroblast collagenase
Q70581313	Metal poison inhibition of carbonic anhydrase
Q70980741	Metal search: a computer program that helps design tetrahedral metal-binding sites
Q44745618	Metal-Induced reversible structural interconversion of human mitochondrial NAD(P)+-dependent malic enzyme.
Q30367299	Method for comparing the structures of protein ligand-binding sites and application for predicting protein-drug interactions.
Q30373197	Method for identification of rigid domains and hinge residues in proteins based on exhaustive enumeration.
Q41679805	Methodology for protein-ligand binding studies: application to a model for drug resistance, the HIV/FIV protease system
Q45945240	Methods for estimation of model accuracy in CASP12.
Q30378820	Methods of model accuracy estimation can help selecting the best models from decoy sets: Assessment of model accuracy estimations in CASP11
Q81508072	Methyl dynamics for understanding hydrophobic core packing of dynamically different motifs of double-stranded RNA binding domain of protein kinase R
Q27648762	Methylene substitution at the alpha-beta bridging position within the phosphate chain of dUDP profoundly perturbs ligand accommodation into the dUTPase active site
Q42183669	Methyltransferases do not work by compression, cratic, or desolvation effects, but by electrostatic preorganization
Q68188222	Michaelis complexes of porcine pancreatic elastase with 7-[(alkylcarbamoyl)amino]-4-chloro-3-ethoxyisocoumarins: translational sampling of inhibitor position and kinetic measurements
Q42623585	Microbial genomes have over 72% structure assignment by the threading algorithm PROSPECTOR_Q.
Q68513082	Microfolding: Conformational probability map for the alanine dipeptide in water from molecular dynamics simulations
Q51318577	Microscopic mechanisms that govern the titration response and pKa values of buried residues in staphylococcal nuclease mutants
Q38988816	Microsecond simulations of mdm2 and its complex with p53 yield insight into force field accuracy and conformational dynamics.
Q36501036	Microsecond simulations of the folding/unfolding thermodynamics of the Trp-cage miniprotein.
Q45784548	Microtube batch protein crystallization: applications to human immunodeficiency virus type 2 (HIV-2) protease and human renin
Q86868220	Microtubules dual chemo and thermo-responsive depolymerization
Q114234883	Milestoning simulation of ligand dissociation from the glycogen synthase kinase 3β
Q52309231	Mimicking a p53-MDM2 interaction based on a stable immunoglobulin-like domain scaffold
Q34192586	Mimicking the action of folding chaperones by Hamiltonian replica-exchange molecular dynamics simulations: application in the refinement of de novo models
Q104583367	Mind the GAP: Purification and characterization of urea resistant GAPDH during extreme dehydration
Q30409794	Minimal ensembles of side chain conformers for modeling protein-protein interactions
Q73182194	Minimal model for studying prion-like folding pathways
Q46813701	Minimal structural requirements for root effect: crystal structure of the cathodic hemoglobin isolated from the antarctic fish Trematomus newnesi
Q81242966	Minimal surface as a model of beta-sheets
Q83365562	Minimizing false positives in kinase virtual screens
Q58847196	Minimum model for the α-helix-β-hairpin transition in proteins
Q57795080	Misfolding of the amyloid β-protein: A molecular dynamics study
Q43014946	Missense mutations in transmembrane domains of proteins: phenotypic propensity of polar residues for human disease
Q46255143	Misunderstanding the preorganization concept can lead to confusions about the origin of enzyme catalysis
Q51320385	Miz-1 and Max compete to engage c-Myc: implication for the mechanism of inhibition of c-Myc transcriptional activity by Miz-1.
Q81388894	Mn/Fe superoxide dismutase interaction fingerprints and prediction of oligomerization and metal cofactor from sequence
Q87542947	Mode coupling points to functionally important residues in myosin II
Q52360157	Model assembly study of the ligand binding by p-hydroxybenzoate hydroxylase: correlation between the calculated binding energies and the experimental dissociation constants
Q30323142	Model building by comparison at CASP3: using expert knowledge and computer automation.
Q30429631	Model building by comparison: a combination of expert knowledge and computer automation.
Q87238479	Model for the allosteric regulation of the Na+/Ca2+ exchanger NCX
Q68837129	Model for the interaction of amphiphilic helices with troponin C and calmodulin
Q28206585	Model for the three-dimensional structure of vitronectin: predictions for the multi-domain protein from threading and docking
Q69841953	Model of a complex between the tetrahemic cytochrome c3 and the ferredoxin I from Desulfovibrio desulfuricans (Norway strain)
Q31913246	Model of the 3-D structure of the GLUT3 glucose transporter and molecular dynamics simulation of glucose transport
Q42680177	Model of the alphaLbeta2 integrin I-domain/ICAM-1 DI interface suggests that subtle changes in loop orientation determine ligand specificity
Q43676067	Model of three-dimensional structure of vitamin D receptor and its binding mechanism with 1alpha,25-dihydroxyvitamin D(3).
Q30373255	Model quality assessment using distance constraints from alignments.
Q43027844	Model-free analysis of a thermophilic Fe(7)S(8) protein compared with a mesophilic Fe(4)S(4) protein
Q58619182	Model-free analysis of a thermophilic Fe7S8 protein compared with a mesophilic Fe4S4 protein
Q73205389	Model-free methods of analyzing domain motions in proteins from simulation: a comparison of normal mode analysis and molecular dynamics simulation of lysozyme
Q47804972	Modeling CAPRI targets 110-120 by template-based and free docking using contact potential and combined scoring function.
Q43269858	Modeling G protein-coupled receptors for structure-based drug discovery using low-frequency normal modes for refinement of homology models: application to H3 antagonists
Q53437310	Modeling GPCR active state conformations: The β2‐adrenergic receptor
Q118958808	Modeling SARS-CoV-2 proteins in the CASP-commons experiment
Q78675892	Modeling alpha-helical coiled-coil interactions: the axial and azimuthal alignment of 1B segments from vimentin intermediate filaments
Q38301628	Modeling and analysis of molecularinteraction between Smurf1-WW2 domain and various isoforms of LIM mineralization protein
Q46991259	Modeling and functional analysis of AEBP1, a transcriptional repressor
Q48960371	Modeling and minimizing CAPRI round 30 symmetrical protein complexes from CASP-11 structural models
Q30159971	Modeling and simulations of a bacterial outer membrane protein: OprF from Pseudomonas aeruginosa
Q92349990	Modeling beta-sheet peptide-protein interactions: Rosetta FlexPepDock in CAPRI rounds 38-45
Q50562576	Modeling complexes of modeled proteins
Q44140902	Modeling conformational change in macromolecules as an elastic deformation
Q92554685	Modeling conformational flexibility of kinases in inactive states
Q50802091	Modeling conformational redox-switch modulation of human succinic semialdehyde dehydrogenase
Q45039418	Modeling correlated main-chain motions in proteins for flexible molecular recognition
Q44898284	Modeling effects of mutations in coiled-coil structures: case study using epidermolysis bullosa simplex mutations in segment 1a of K5/K14 intermediate filaments
Q51900428	Modeling ensembles of transmembrane beta-barrel proteins
Q40927134	Modeling evolution of hydrogen bonding and stabilization of transition states in the process of cocaine hydrolysis catalyzed by human butyrylcholinesterase
Q57135724	Modeling implicit reorganization in continuum descriptions of protein-protein interactions
Q51986757	Modeling loop reorganization free energies of acetylcholinesterase: a comparison of explicit and implicit solvent models
Q52416614	Modeling microdomains: the surface area of globin helices
Q39352554	Modeling oblong proteins and water-mediated interfaces with RosettaDock in CAPRI rounds 28-35.
Q40950808	Modeling of a five-stranded coiled coil structure for the assembly domain of the cartilage oligomeric matrix protein
Q74631429	Modeling of acanthoxin A1, a PLA2 enzyme from the venom of the common death adder (Acanthophis antarcticus)
Q68079018	Modeling of agonist binding to the ligand-gated ion channel superfamily of receptors
Q71774348	Modeling of halorhodopsin and rhodopsin based on bacteriorhodopsin
Q52244720	Modeling of inhibitor–metalloenzyme interactions and selectivity using molecular mechanics grounded in quantum chemistry
Q73521264	Modeling of ion permeation in calcium and sodium channel selectivity filters
Q30366129	Modeling of metal interaction geometries for protein-ligand docking.
Q40643073	Modeling of peptides connecting the ligand-binding and transmembrane domains in the GluR2 glutamate receptor.
Q47804826	Modeling of protein complexes in CAPRI Round 37 using template-based approach combined with model selection.
Q58489158	Modeling of protein interactions in genomes
Q74054756	Modeling of protein interactions in genomes
Q71856538	Modeling of serpin-protease complexes: antithrombin-thrombin, alpha 1-antitrypsin (358Met-->Arg)-thrombin, alpha 1-antitrypsin (358Met-->Arg)-trypsin, and antitrypsin-elastase
Q67562106	Modeling of substrate and inhibitor binding to phospholipase A2
Q68091115	Modeling of the human intercellular adhesion molecule-1, the human rhinovirus major group receptor
Q46345012	Modeling of the metallo-beta-lactamase from B. fragilis: structural and dynamic effects of inhibitor binding.
Q51970536	Modeling oligomers with Cn or Dn symmetry: application to CAPRI target 10.
Q92454873	Modeling post-translational modifications and cancer-associated mutations that impact the heterochromatin protein 1α-importin α heterodimers
Q47566911	Modeling protein assemblies: Critical Assessment of Predicted Interactions (CAPRI) 15 years hence.: 6TH CAPRI evaluation meeting April 17-19 Tel-Aviv, Israel
Q52015271	Modeling protein complexes with BiGGER.
Q51934987	Modeling protein conformational ensembles: from missing loops to equilibrium fluctuations.
Q74015793	Modeling protein density of states: additive hydrophobic effects are insufficient for calorimetric two-state cooperativity
Q89796250	Modeling protein interactions and complexes in CAPRI: Seventh CAPRI evaluation meeting, April 3-5 EMBL-EBI, Hinxton, UK
Q36185366	Modeling protein recognition of carbohydrates
Q39172517	Modeling protein-protein and protein-peptide complexes: CAPRI 6th edition
Q92318885	Modeling protein-protein, protein-peptide, and protein-oligosaccharide complexes: CAPRI 7th edition
Q84594092	Modeling reaction routes from rhodopsin to bathorhodopsin
Q51970532	Modeling side-chains using molecular dynamics improve recognition of binding region in CAPRI targets
Q30341350	Modeling structurally variable regions in homologous proteins with rosetta.
Q33304501	Modeling the accessible conformations of the intrinsically unstructured transactivation domain of p53.
Q46604797	Modeling the anti-CEA antibody combining site by homology and conformational search
Q46109010	Modeling the biochemical differences between rabbit muscle and human liver phosphorylase
Q48036962	Modeling the interaction between aldolase and the thrombospondin-related anonymous protein, a key connection of the malaria parasite invasion machinery
Q30428829	Modeling the paramyxovirus hemagglutinin-neuraminidase protein
Q42951624	Modeling the possible conformations of the extracellular loops in G-protein-coupled receptors
Q52348356	Modeling the quinone-B binding site of the photosystem-II reaction center using notions of complementarity and contact-surface between atoms
Q54085346	Modeling the role of disulfide bonds in protein folding: Entropic barriers and pathways
Q50945170	Modeling the structure of mAb 14B7 bound to the anthrax protective antigen
Q30327518	Modeling the third loop of short-chain snake venom neurotoxins: roles of the short-range and long-range interactions.
Q40553682	Modeling three-dimensional protein structures for CASP5 using the 3D-SHOTGUN meta-predictors
Q52141277	Modeling three-dimensional protein structures for amino acid sequences of the CASP3 experiment using sequence-derived predictions
Q46825707	Modeling truncated hemoglobin vibrational dynamics
Q27629207	Modeling, mutagenesis, and structural studies on the fully conserved phosphate-binding loop (loop 8) of triosephosphate isomerase: toward a new substrate specificity
Q41607225	Modelling of factor Xa-inhibitor complexes: a computational flexible docking approach
Q30159495	Modelling of the ABL and ARG proteins predicts two functionally critical regions that are natively unfolded
Q48001234	Modelling repressor proteins docking to DNA.
Q73233205	Modelling the catalytic reaction in human aldose reductase
Q30195745	Modelling the three-dimensional structure and electrostatic potential field of the two Cu,Zn superoxide dismutase variants from Xenopus laevis.
Q52505237	Models of delta-hemolysin membrane channels and crystal structures
Q30155996	Models of membrane‐bound Alzheimer's Abeta peptide assemblies
Q77142609	Models of natural mutations including site heterogeneity
Q91797647	Modification of lactoferrin by peroxynitrite reduces its antibacterial activity and changes protein structure
Q40648632	Modifications to canonical structure sequence patterns: analysis for L1 and L3.
Q41736267	Modified genetic algorithm resolves ambiguous NOE restraints and reduces unsightly NOE violations
Q46020528	Modular coenzyme specificity: a domain-swopped chimera of glutamate dehydrogenase.
Q30379187	Modularity of intrinsic disorder in the human proteome.
Q82452429	Modulated nicking endonuclease function by the N‐terminal extended region of the smr domain in human Bcl‐3 binding protein
Q30351986	Modulating the folding stability and ligand binding affinity of Pin1 WW domain by proline ring puckering.
Q72154717	Modulation of DNA-binding specificity within the nuclear receptor family by substitutions at a single amino acid position
Q98830084	Modulation of GCSF Conformation and Receptor Binding by Methionine Oxidation
Q35706925	Modulation of HIV protease flexibility by the T80N mutation
Q58112058	Modulation of glucan-enzyme interactions by domain V in GTF-SI from Streptococcus mutans
Q38299891	Modulation of human cytidine deaminase by specific aminoacids involved in the intersubunit interactions
Q37221295	MolAxis: efficient and accurate identification of channels in macromolecules
Q98937838	Molecular Dynamics Analysis of The Binding of Human Interleukin-6 with Interleukin-6 α-Receptor
Q101219650	Molecular Dynamics Simulations Identify the Regions of Compromised Thermostability in SazCA
Q30360596	Molecular adaptation strategies to high temperature and thermal denaturation mechanism of the D-trehalose/D-maltose-binding protein from the hyperthermophilic archaeon Thermococcus litoralis.
Q91294615	Molecular and structural bases of interaction between extracellular domains of nectin-2 and N-cadherin
Q40533093	Molecular aspects of the interaction between Mason-Pfizer monkey virus matrix protein and artificial phospholipid membrane.
Q27652190	Molecular basis for dimer formation of TRβ variant D355R
Q27642891	Molecular basis for redox-Bohr and cooperative effects in cytochrome c3 from Desulfovibrio desulfuricans ATCC 27774: crystallographic and modeling studies of oxidized and reduced high-resolution structures at pH 7.6
Q52389865	Molecular basis of cooperativity in protein folding. IV. CORE: a general cooperative folding model
Q72867725	Molecular basis of cooperativity in protein folding. V. Thermodynamic and structural conditions for the stabilization of compact denatured states
Q90564501	Molecular basis of drug resistance in smoothened receptor: An in silico study of protein resistivity and specificity
Q51625612	Molecular basis of inhibitory peptide maurotoxin recognizing Kv1.2 channel explored by ZDOCK and molecular dynamic simulations
Q27676867	Molecular basis of the fructose-2,6-bisphosphatase reaction of PFKFB3: Transition state and the C-terminal function
Q30427366	Molecular collapse: the rate-limiting step in two-state cytochrome c folding
Q46551396	Molecular damage in Fabry disease: characterization and prediction of alpha-galactosidase A pathological mutations
Q51989293	Molecular definitions of fatty acid hydroxylases in Arabidopsis thaliana
Q47552574	Molecular details of spontaneous insertion and interaction of HCV non-structure 3 protease protein domain with PIP2-containing membrane.
Q40172670	Molecular determinants of sarco/endoplasmic reticulum calcium ATPase inhibition by hydroquinone-based compounds
Q44179888	Molecular determinants of thapsigargin binding by SERCA Ca2+-ATPase: a computational docking study
Q57531358	Molecular determinants of the ATP hydrolysis asymmetry of the CCT chaperonin complex
Q27656001	Molecular determinants of the pKa values of Asp and Glu residues in staphylococcal nuclease
Q46770745	Molecular docking of balanol to dynamics snapshots of protein kinase A.
Q81230766	Molecular docking study of the interactions between the thioesterase domain of human fatty acid synthase and its ligands
Q52306147	Molecular docking using surface complementarity
Q38302828	Molecular domain organization of BldD, an essential transcriptional regulator for developmental process of Streptomyces coelicolor A3(2).
Q85281477	Molecular dynamic studies on the impact of mutations on the structure, stability, and N-terminal orientation of annexin A1: implications for membrane aggregation
Q30559805	Molecular dynamics and accuracy of NMR structures: effects of error bounds and data removal
Q68036476	Molecular dynamics characterization of the active cavity of carboxypeptidase A and some of its inhibitor adducts
Q57138607	Molecular dynamics effects on protein electrostatics
Q30371408	Molecular dynamics guided study of salt bridge length dependence in both fluorinated and non-fluorinated parallel dimeric coiled-coils.
Q90267310	Molecular dynamics investigation of a redox switch in the anti-HIV protein SAMHD1
Q53323973	Molecular dynamics investigation of the ionic liquid/enzyme interface: application to engineering enzyme surface charge
Q84922890	Molecular dynamics modeling of tubulin C-terminal tail interactions with the microtubule surface
Q27667125	Molecular dynamics of EF‐G during translocation
Q68151703	Molecular dynamics of HIV-1 protease
Q43557768	Molecular dynamics of HIV-1 reverse transcriptase indicates increased flexibility upon DNA binding
Q30157532	Molecular dynamics of amicyanin reveals a conserved dynamical core for blue copper proteins
Q43245874	Molecular dynamics of leucine and dopamine transporter proteins in a model cell membrane lipid bilayer
Q39531209	Molecular dynamics of mouse and Syrian hamster PrP: implications for activity
Q33462407	Molecular dynamics of the structural changes of helical peptides induced by pressure
Q53455831	Molecular dynamics of water and monovalent-ions transportation mechanisms of pentameric sarcolipin
Q73594404	Molecular dynamics simulation accurately predicts the experimentally-observed distributions of the (C, N, O) protein atoms around water molecules and sodium ions
Q83365559	Molecular dynamics simulation of Leishmania major surface metalloprotease GP63 (leishmanolysin)
Q43670289	Molecular dynamics simulation of PNPLA3 I148M polymorphism reveals reduced substrate access to the catalytic cavity
Q84398083	Molecular dynamics simulation of SRP GTPases: towards an understanding of the complex formation from equilibrium fluctuations
Q82621430	Molecular dynamics simulation of conformational heterogeneity in transportin 1
Q30596356	Molecular dynamics simulation of hen egg white lysozyme: a test of the GROMOS96 force field against nuclear magnetic resonance data
Q72061285	Molecular dynamics simulation of hydration in myoglobin
Q59576384	Molecular dynamics simulation of solvated azurin: Correlation between surface solvent accessibility and water residence times
Q38330299	Molecular dynamics simulation of sucrose- and trehalose-coated carboxy-myoglobin
Q46489552	Molecular dynamics simulation of the acidic compact state of apomyoglobin from yellowfin tuna.
Q57795191	Molecular dynamics simulation of the aggregation of the core-recognition motif of the islet amyloid polypeptide in explicit water
Q52375019	Molecular dynamics simulation of the docking of substrates to proteins
Q87374682	Molecular dynamics simulation of the phosphorylation-induced conformational changes of a tau peptide fragment
Q92029532	Molecular dynamics simulation of tropomyosin bound to actins/myosin in the closed and open states
Q60218551	Molecular dynamics simulation of β2-microglobulin in denaturing and stabilizing conditions
Q44296015	Molecular dynamics simulation reveals a surface salt bridge forming a kinetic trap in unfolding of truncated Staphylococcal nuclease
Q46971345	Molecular dynamics simulation study for LRH-1: interaction with fragments of SHP and function of phospholipid ligand
Q40333546	Molecular dynamics simulation study of the "stay or leave" problem for two magnesium ions in gene transcription.
Q47662738	Molecular dynamics simulation, binding free energy calculation and unbinding pathway analysis on selectivity difference between FKBP51 and FKBP52: Insight into the molecular mechanism of isoform selectivity.
Q41909739	Molecular dynamics simulations and functional characterization of the interactions of the PAR2 ectodomain with factor VIIa
Q54233905	Molecular dynamics simulations elucidate the mode of protein recognition by Skp1 and the F-box domain in the SCF complex
Q30157923	Molecular dynamics simulations from putative transition states of alpha-spectrin SH3 domain
Q85651656	Molecular dynamics simulations indicate that tyrosineB10 limits motions of distal histidine to regulate CO binding in soybean leghemoglobin
Q50923985	Molecular dynamics simulations of HIV-1 protease monomer: Assembly of N-terminus and C-terminus into beta-sheet in water solution.
Q80278826	Molecular dynamics simulations of Hydrogenobacter thermophilus cytochrome c552: comparisons of the wild-type protein, a b-type variant, and the apo state
Q46827745	Molecular dynamics simulations of LysRS: an asymmetric state.
Q73365503	Molecular dynamics simulations of N-terminal peptides from a nucleotide binding protein
Q74449646	Molecular dynamics simulations of a double unit cell in a protein crystal: volume relaxation at constant pressure and correlation of motions between the two unit cells
Q41895411	Molecular dynamics simulations of a helicase
Q30167944	Molecular dynamics simulations of a highly charged peptide from an SH3 domain: possible sequence-function relationship
Q30164798	Molecular dynamics simulations of a protein model in uniform and elongational flows
Q52360151	Molecular dynamics simulations of alcohol dehydrogenase with a four- or five-coordinate catalytic zinc ion.
Q48065730	Molecular dynamics simulations of apo, holo, and inactivator bound GABA-at reveal the role of active site residues in PLP dependent enzymes
Q52133674	Molecular dynamics simulations of beta-hairpin folding
Q42634253	Molecular dynamics simulations of domain motions of substrate-free S-adenosyl- L-homocysteine hydrolase in solution
Q52018275	Molecular dynamics simulations of enhanced green fluorescent proteins: effects of F64L, S65T and T203Y mutations on the ground-state proton equilibria
Q31966089	Molecular dynamics simulations of epidermal growth factor and transforming growth factor-alpha structures in water
Q46899110	Molecular dynamics simulations of ethanol binding to the transmembrane domain of the glycine receptor: implications for the channel potentiation mechanism
Q34310983	Molecular dynamics simulations of galectin‐1‐oligosaccharide complexes reveal the molecular basis for ligand diversity
Q52535439	Molecular dynamics simulations of human alpha-lactalbumin: changes to the structural and dynamical properties of the protein at low pH.
Q42647267	Molecular dynamics simulations of human butyrylcholinesterase.
Q77314243	Molecular dynamics simulations of human carbonic anhydrase II: Insight into experimental results and the role of solvation
Q78140806	Molecular dynamics simulations of human glutathione transferase P1-1: analysis of the induced-fit mechanism by GSH binding
Q78140812	Molecular dynamics simulations of human glutathione transferase P1-1: conformational fluctuations of the apo-structure
Q30770627	Molecular dynamics simulations of peptides and proteins with a continuum electrostatic model based on screened Coulomb potentials.
Q30887031	Molecular dynamics simulations of peptides containing an unnatural amino acid: dimerization, folding, and protein binding
Q78136342	Molecular dynamics simulations of polypeptide conformations in water: A comparison of alpha, beta, and poly(pro)II conformations
Q41810800	Molecular dynamics simulations of ribonuclease T1: comparison of the free enzyme and the 2' GMP-enzyme complex
Q36682552	Molecular dynamics simulations of rubredoxin from Clostridium pasteurianum: changes in structure and electrostatic potential during redox reactions
Q47596399	Molecular dynamics simulations of structural changes during procaspase 3 activation
Q71543068	Molecular dynamics simulations of synthetic peptide folding
Q30560225	Molecular dynamics simulations of the Ras:Raf and Rap:Raf complexes
Q61644569	Molecular dynamics simulations of the active matrix metalloproteinase-2: Positioning of the N-terminal fragment and binding of a small peptide substrate
Q43956367	Molecular dynamics simulations of the acyl-enzyme and the tetrahedral intermediate in the deacylation step of serine proteases
Q50452706	Molecular dynamics simulations of the auxin-binding protein 1 in complex with indole-3-acetic acid and naphthalen-1-acetic acid
Q43694844	Molecular dynamics simulations of the conformational changes of the glutamate receptor ligand-binding core in the presence of glutamate and kainate.
Q31035927	Molecular dynamics simulations of the cytochrome c3-rubredoxin complex from Desulfovibrio vulgaris
Q83980840	Molecular dynamics simulations of the hydrophobin SC3 at a hydrophobic/hydrophilic interface
Q38548814	Molecular dynamics simulations of transitions for ECD epidermal growth factor receptors show key differences between human and drosophila forms of the receptors.
Q72635007	Molecular dynamics simulations of trp apo- and holorepressors: domain structure and ligand-protein interaction
Q47266895	Molecular dynamics simulations on interaction between bacterial proteins: Implication on pathogenic activities.
Q30399511	Molecular dynamics simulations on networks of heparin and collagen.
Q83782509	Molecular dynamics simulations reveal structural coordination of Ffh‐FtsY heterodimer toward GTPase activation
Q39038055	Molecular dynamics simulations reveal structural insights into inhibitor binding modes and functionality in human Group IIA phospholipase A2.
Q30353042	Molecular dynamics simulations reveal that apo-HisJ can sample a closed conformation.
Q91142570	Molecular dynamics simulations to the bidirectional adhesion signaling pathway of integrin αV β3
Q53383110	Molecular dynamics studies of hexamers of amyloid-beta peptide (16-35) and its mutants: influence of charge states on amyloid formation
Q30652050	Molecular dynamics studies of the energetics of translocation in model T7 RNA polymerase elongation complexes
Q44324122	Molecular dynamics studies on HIV-1 protease drug resistance and folding pathways
Q72510988	Molecular dynamics studies on mutants of Cu,Zn superoxide dismutase: the functional role of charged residues in the electrostatic loop VII
Q83003939	Molecular dynamics studies on structure and dynamics of phospholamban monomer and pentamer in membranes
Q30355077	Molecular dynamics study of HIV-1 RT-DNA-nevirapine complexes explains NNRTI inhibition and resistance by connection mutations
Q46794956	Molecular dynamics study of Pseudomonas aeruginosa lectin-II complexed with monosaccharides
Q51945037	Molecular dynamics study of a calmodulin-like protein with an IQ peptide: spontaneous refolding of the protein around the peptide
Q77615161	Molecular dynamics study of a hyperthermophilic and a mesophilic rubredoxin
Q31996390	Molecular dynamics study of calbindin D9k in the apo and singly and doubly calcium-loaded states
Q50622453	Molecular dynamics study of chemically engineered green fluorescent protein mutants: comparison of intramolecular fluorescence resonance energy transfer rate
Q79750721	Molecular dynamics study of conformational changes in human serum albumin by binding of fatty acids
Q77142603	Molecular dynamics study of femtosecond events in photoactive yellow protein after photoexcitation of the chromophore
Q71074630	Molecular dynamics study of glucocorticoid receptor-DNA binding
Q43167687	Molecular dynamics study of interaction and substrate channeling between neuron-specific enolase and B-type phosphoglycerate mutase
Q93196984	Molecular dynamics study of interactions between polymorphic actin filaments and gelsolin segment-1
Q56997534	Molecular dynamics study of onset of water gelation around the collagen triple helix
Q52306162	Molecular dynamics study of phospholipase A2 on a membrane surface
Q68837137	Molecular dynamics study of secondary structure motions in proteins: application to myohemerythrin
Q84484847	Molecular dynamics study of small molecule inhibitors of the Bcl‐2 family
Q72890883	Molecular dynamics study of structure and stability of a model coiled coil
Q52224074	Molecular dynamics study of the proposed beta-hairpin form of the switch domain from HIV1 gp120 alone and complexed with an inhibitor of CD4 binding
Q57269351	Molecular dynamics study of the stabilities of consensus designed ankyrin repeat proteins
Q30350921	Molecular dynamics study of water penetration in staphylococcal nuclease.
Q30152917	Molecular dynamics study on folding and allostery in RfaH.
Q30351821	Molecular dynamics study on the folding and metallation of the individual domains of metallothionein.
Q43676069	Molecular engineering of a polymer of tetrameric hemoglobins
Q42914294	Molecular function prediction for a family exhibiting evolutionary tendencies toward substrate specificity swapping: recurrence of tyrosine aminotransferase activity in the Iα subfamily
Q24301390	Molecular insight into substrate recognition by human cytosolic sialidase NEU2
Q36027178	Molecular insights into substrate specificity of prostate specific antigen through structural modeling
Q37968625	Molecular interactions in protein crystals: solvent accessible surface and stability
Q74527941	Molecular mapping of thrombin-receptor interactions
Q73598264	Molecular mechanic study of nerve agentO-ethylS-[2-(diisopropylamino)ethyl]methylphosphonothioate (VX) bound to the active site ofTorpedo californica acetylcholinesterase
Q58072092	Molecular mechanics simulations of a conformational rearrangement ofD-xylose in the active site ofD-xylose isomerase
Q39784629	Molecular mechanism of allosteric communication in the human PPARalpha-RXRalpha heterodimer
Q44482709	Molecular mechanism of substrate specificity in the bacterial neutral amino acid transporter LeuT.
Q85181911	Molecular mechanism of β-sheet self-organization at water-hydrophobic interfaces
Q36791136	Molecular mechanisms and design principles for promiscuous inhibitors to avoid drug resistance: lessons learned from HIV-1 protease inhibition.
Q73844958	Molecular mechanisms of microheterogeneity-induced defect formation in ferritin crystallization
Q46885324	Molecular mechanisms of pH-driven conformational transitions of proteins: insights from continuum electrostatics calculations of acid unfolding
Q71671452	Molecular mechanisms of pressure induced conformational changes in BPTI
Q46937887	Molecular modeling and inhibitory activity of cowpea cystatin against bean bruchid pests
Q40487987	Molecular modeling and redesign of alginate lyase from Pseudomonas aeruginosa for accelerating CRPA biofilm degradation
Q70980729	Molecular modeling indicates that homodimers form the basis for intermediate filament assembly from human and mouse epidermal keratins
Q68137858	Molecular modeling of an antigenic complex between a viral peptide and a class I major histocompatibility glycoprotein
Q46560918	Molecular modeling of cardiac glycoside binding by the human sequence monoclonal antibody 1B3.
Q57127563	Molecular modeling of hair keratin/peptide complex: Using MM-PBSA calculations to describe experimental binding results
Q56984897	Molecular modeling of prohibitin domains
Q44898273	Molecular modeling of protein function regions.
Q33895934	Molecular modeling of substrate binding in wild-type and mutant Corynebacteria 2,5-diketo-D-gluconate reductases
Q44237500	Molecular modeling of the amphipathic helices of the plasma apolipoproteins
Q35875508	Molecular modeling of the binding modes of the iron-sulfur protein to the Jac1 co-chaperone from Saccharomyces cerevisiae by all-atom and coarse-grained approaches
Q80514486	Molecular modeling of the core of Abeta amyloid fibrils
Q33304500	Molecular modeling of the second extracellular loop of G-protein coupled receptors and its implication on structure-based virtual screening
Q36841483	Molecular modeling of vimentin filament assembly
Q86693970	Molecular modeling reveals binding interface of γ-tubulin with GCP4 and interactions with noscapinoids
Q44515165	Molecular modeling studies on CNG channel from bovine retinal rod: a structural model of the cyclic nucleotide-binding domain
Q44784454	Molecular modeling study of the editing active site of Escherichia coli leucyl-tRNA synthetase: two amino acid binding sites in the editing domain
Q92926898	Molecular modeling study on the differential microtubule-stabilizing effect in singly- and doubly-bonded complexes with peloruside A and paclitaxel
Q52080525	Molecular modelling of Trematomus newnesi Hb 1: insights for a lowered oxygen affinity and lack of root effect
Q44125124	Molecular motions and conformational changes of HPPK.
Q33875834	Molecular organization, structural features, and ligand binding characteristics of CD44, a highly variable cell surface glycoprotein with multiple functions
Q34410331	Molecular physiology of the tensin brotherhood of integrin adaptor proteins
Q27644738	Molecular properties of two proteins homologous to PduO-type ATP:cob(I)alamin adenosyltransferase from Sulfolobus tokodaii
Q80045457	Molecular recognition mechanism of FK506 binding protein: an all-electron fragment molecular orbital study
Q45076941	Molecular recognition of aldehydes by aldehyde dehydrogenase and mechanism of nucleophile activation.
Q79992387	Molecular simulations bring new insights into flavonoid/quercetinase interaction modes
Q46462901	Molecular simulations enlighten the binding mode of quercetin to lipoxygenase-3.
Q61641978	Molecular simulations of β-lactoglobulin complexed with fatty acids reveal the structural basis of ligand affinity to internal and possible external binding sites
Q79757155	Molecular simulations reveal a new entry site in quercetin 2,3-dioxygenase. A pathway for dioxygen?
Q72668319	Molecular skins: a new concept for quantitative shape matching of a protein with its small molecule mimics
Q38290571	Molecular strategies for protein stabilization: the case of a trehalose/maltose-binding protein from Thermus thermophilus.
Q39699464	Molecular structure and evolution of adrenergic and cholinergic receptors
Q51960093	Molecular surface generation using a variable-radius solvent probe
Q29035652	Molecular surface representations by sparse critical points
Q71623213	Molecular systematics in 3D: the classification of protein structures. Paris, April 9-11, 1996
Q30327337	Molecular-dynamics simulation of the beta domain of metallothionein with a semi-empirical treatment of the metal core.
Q45125265	Molego-based definition of the architecture and specificity of metal-binding sites
Q35971266	Molprobity's ultimate rotamer-library distributions for model validation
Q44165220	Molten globule of bovine alpha-lactalbumin at neutral pH induced by heat, trifluoroethanol, and oleic acid: a comparative analysis by circular dichroism spectroscopy and limited proteolysis
Q73319295	Molten globule state of equine beta-lactoglobulin
Q59239010	Monitoring transient events in infrared spectra using local mode analysis
Q27654883	Monomeric tRNA (m(7)G46) methyltransferase from Escherichia coli presents a novel structure at the function-essential insertion
Q30731518	Monophyly of class I aminoacyl tRNA synthetase, USPA, ETFP, photolyase, and PP-ATPase nucleotide-binding domains: implications for protein evolution in the RNA.
Q52418353	Monte Carlo docking of oligopeptides to proteins
Q30332738	Monte Carlo estimation of the number of possible protein folds: Effects of sampling bias and folds distributions
Q51911565	Monte Carlo folding of trans-membrane helical peptides in an implicit generalized Born membrane
Q67562104	Monte Carlo minimization with thermalization for global optimization of polypeptide conformations in cartesian coordinate space
Q30398315	Monte Carlo replica-exchange based ensemble docking of protein conformations
Q79236250	Monte Carlo sampling of near-native structures of proteins with applications
Q74267467	Monte Carlo simulation of denaturation of adsorbed proteins
Q73594379	Monte Carlo simulation of diffusion of adsorbed proteins
Q52251889	Monte Carlo simulation of protein folding with orientation-dependent monomer–monomer interactions
Q30429718	Monte Carlo simulation of the kinetics of protein adsorption
Q45987283	Monte Carlo simulations of protein folding. I. Lattice model and interaction scheme.
Q30421319	Monte Carlo simulations of protein folding. II. Application to protein A, ROP, and crambin
Q43814574	Monte Carlo simulations of the peptide recognition at the consensus binding site of the constant fragment of human immunoglobulin G: the energy landscape analysis of a hot spot at the intermolecular interface
Q73521274	Monte Carlo-minimized energy profile of estradiol in the ligand-binding tunnel of 17 beta-hydroxysteroid dehydrogenase: atomic mechanisms of steroid recognition
Q58037807	More compact protein globules exhibit slower folding rates
Q51351315	Motion of transfer RNA from the A/T state into the A‐site using docking and simulations
Q43088941	Motional timescale predictions by molecular dynamics simulations: case study using proline and hydroxyproline sidechain dynamics.
Q36016551	Multi-LZerD: multiple protein docking for asymmetric complexes
Q28914723	Multi-constraint computational design suggests that native sequences of germline antibody H3 loops are nearly optimal for conformational flexibility
Q56834871	Multi-method global analysis of thermodynamics and kinetics in reconstitution of monellin
Q33684624	Multi-scale characterization of the energy landscape of proteins with application to the C3D/Efb-C complex
Q51171122	Multi-template approach to modeling engineered disulfide bonds
Q42039279	Multibody coarse-grained potentials for native structure recognition and quality assessment of protein models
Q95650714	Multicopper oxidases: modular structure, sequence space and evolutionary relationships
Q73233226	Multifunctional enzymes and evolution of biosynthetic pathways: retro-evolution by jumps
Q93120338	Multimapping confounds ribosome profiling analysis: A case-study of the Hsp90 molecular chaperone
Q30352314	Multipass membrane protein structure prediction using Rosetta
Q51100258	Multiple Gaussian network modes alignment reveals dynamically variable regions: the hemoglobin case
Q33283213	Multiple asparagine deamidation of Bacillus anthracis protective antigen causes charge isoforms whose complexity correlates with reduced biological activity
Q87624491	Multiple conformational states and gate opening of outer membrane protein TolC revealed by molecular dynamics simulations
Q45946454	Multiple conformational states of a new hematopoietic cytokine (megakaryocyte growth and development factor): pH- and urea-induced denaturation
Q68704287	Multiple conformations of amino acid residues in ribonuclease A
Q54026445	Multiple copy sampling: rigid versus flexible protein
Q58670508	Multiple display of a protein domain on a bacterial polymeric scaffold
Q54549089	Multiple drugs and multiple targets: An analysis of the electrostatic determinants of binding between non‐nucleoside HIV‐1 reverse transcriptase inhibitors and variants of HIV‐1 RT
Q81523628	Multiple folding mechanisms of protein ubiquitin
Q39000654	Multiple helical conformations of the helix-turn-helix region revealed by NOE-restrained MD simulations of tryptophan aporepressor, TrpR.
Q73713054	Multiple linear regression for protein secondary structure prediction
Q30352690	Multiple mapping method: a novel approach to the sequence-to-structure alignment problem in comparative protein structure modeling.
Q27729294	Multiple modes of ligand recognition: crystal structures of cyclin-dependent protein kinase 2 in complex with ATP and two inhibitors, olomoucine and isopentenyladenine
Q48211957	Multiple molecular dynamics simulations of human LOX-1 and Trp150Ala mutant reveal the structural determinants causing the full deactivation of the receptor
Q83203029	Multiple molecular dynamics simulations of human p450 monooxygenase CYP2C9: the molecular basis of substrate binding and regioselectivity toward warfarin
Q27684751	Multiple polymer architectures of human polyhomeotic homolog 3 sterile alpha motif
Q30168197	Multiple protein folding nuclei and the transition state ensemble in two-state proteins
Q29615743	Multiple protein sequence alignment from tertiary structure comparison: assignment of global and residue confidence levels
Q55070133	Multiple proton relay routes in the reaction mechanism of RNAP II: assessing the effect of structural model.
Q27654183	Multiple solvent crystal structures of ribonuclease A: an assessment of the method
Q46356926	Multiple time step diffusive Langevin dynamics for proteins
Q70618652	Multiple-site titration and molecular modeling: two rapid methods for computing energies and forces for ionizable groups in proteins
Q38272896	Multiscale characterization of protein conformational ensembles
Q83630174	Multiscale modeling of cellular actin filaments: from atomistic molecular to coarse-grained dynamics
Q51984585	Multiscale modeling of macromolecular conformational changes combining concepts from rigidity and elastic network theory
Q51789201	Multiscale modeling of structural dynamics underlying force generation and product release in actomyosin complex
Q42915927	Multiscale simulations of protein landscapes: using coarse-grained models as reference potentials to full explicit models
Q54284917	Multivariate sequence analysis reveals additional function impacting residues in the SDR superfamily
Q125341923	Multi‐state modeling of G‐protein coupled receptors at experimental accuracy
Q31171716	MurD ligase from E. coli: Tetrahedral intermediate formation study by hybrid quantum mechanical/molecular mechanical replica path method.
Q27680679	Murine norovirus protein NS1/2 aspartate to glutamate mutation, sufficient for persistence, reorients side chain of surface exposed tryptophan within a novel structured domain
Q34993607	Muscle FBPase is targeted to nucleus by its 203KKKGK207 sequence
Q38319809	Mutagenesis at Pro309 of single-chain urokinase-type plasminogen activator alters its catalytic properties
Q31101709	Mutagenesis data in the automated prediction of transmembrane helix dimers
Q80867933	Mutagenesis study of rice nonspecific lipid transfer protein 2 reveals residues that contribute to structure and ligand binding
Q35531134	Mutagenic dissection of hemoglobin cooperativity: effects of amino acid alteration on subunit assembly of oxy and deoxy tetramers
Q30367653	Mutant bovine odorant-binding protein: Temperature affects the protein stability and dynamics as revealed by infrared spectroscopy and molecular dynamics simulations.
Q68704277	Mutant forms of staphylococcal nuclease with altered patterns of guanidine hydrochloride and urea denaturation
Q38329720	Mutating the charged residues in the binding pocket of cellular retinoic acid-binding protein simultaneously reduces its binding affinity to retinoic acid and increases its thermostability
Q43027621	Mutation design of a thermophilic Rubisco based on three-dimensional structure enhances its activity at ambient temperature
Q91786960	Mutation in a flexible linker modulates binding affinity for modular complexes
Q30426887	Mutation matrices and physical-chemical properties: correlations and implications
Q54465965	Mutation of Phe102 to Ser in the carboxyl terminal helix of Escherichia coli thioredoxin affects the stability and processivity of T7 DNA polymerase.
Q45161404	Mutational analysis of domain antibodies reveals aggregation hotspots within and near the complementarity determining regions
Q44972183	Mutational analysis of m-values as a strategy to identify cold-resistant substructures of the protein ensemble
Q59137790	Mutational analysis of the pro-peptide of a marine intracellular subtilisin protease supports its role in inhibition
Q36755108	Mutational tests of the NMR-docked structure of the staphylococcal nuclease-metal-3',5'-pdTp complex
Q46846115	Mutations in alpha-helical solvent-exposed sites of eglin c have long-range effects: evidence from molecular dynamics simulations
Q48124740	MxaJ structure reveals a periplasmic binding protein-like architecture with unique secondary structural elements
Q44566267	Mycobacterium smegmatis RecA protein is structurally similar to but functionally distinct from Mycobacterium tuberculosis RecA.
Q30155475	Mycobacterium tuberculosis Rv0899 defines a family of membrane proteins widespread in nitrogen‐fixing bacteria
Q47589435	Mycobacterium tuberculosis UvrB forms dimers in solution and interacts with UvrA in the absence of ligands.
Q36479553	Mycobacterium tuberculosis copper-regulated protein SocB is an intrinsically disordered protein that folds upon interaction with a synthetic phospholipid bilayer
Q46753794	Mycobacterium tuberculosis isocitrate lyase (MtbIcl): role of divalent cations in modulation of functional and structural properties
Q27658108	Mycobacterium tuberculosisRv2704 is a member of the YjgF/YER057c/UK114 family
Q47236477	Myosin flexibility: structural domains and collective vibrations.
Q44706738	N-H...O, O-H...O, and C-H...O hydrogen bonds in protein-ligand complexes: strong and weak interactions in molecular recognition
Q40063167	N-linked glycans of the human insulin receptor and their distribution over the crystal structure
Q33583554	N-terminal strands of filamin Ig domains act as a conformational switch under biological forces
Q27688980	N-terminal β-strand swapping in a consensus-derived alternative scaffold driven by stabilizing hydrophobic interactions
Q54440059	NAD+-dependent DNA ligase (Rv3014c) from Mycobacterium tuberculosis: novel structure-function relationship and identification of a specific inhibitor.
Q28486332	NAD+-dependent DNA ligases of Mycobacterium tuberculosis and Streptomyces coelicolor
Q43900314	NADH interactions with WT- and S94A-acyl carrier protein reductase from Mycobacterium tuberculosis: an ab initio study
Q34064610	NADP-dependent enzymes. I: Conserved stereochemistry of cofactor binding
Q73326564	NADP-dependent enzymes. II: Evolution of the mono- and dinucleotide binding domains
Q27697656	NF023 binding to XIAP-BIR1: searching drugs for regulation of the NF-κB pathway
Q46676359	NMR assignments of tryptophan residue in apo and holo LBD-rVDR.
Q43208254	NMR characterization of an engineered domain fusion between maltose binding protein and TEM1 beta-lactamase provides insight into its structure and allosteric mechanism.
Q92926930	NMR characterization of conformational fluctuations and noncovalent interactions of SUMO protein from Drosophila melanogaster (dSmt3)
Q30937711	NMR docking of a substrate into the X-ray structure of staphylococcal nuclease
Q72589779	NMR docking of the competitive inhibitor thymidine 3',5'-diphosphate into the X-ray structure of staphylococcal nuclease
Q38777104	NMR identification of the binding surfaces involved in the Salmonella and Shigella Type III secretion tip-translocon protein-protein interactions
Q30646851	NMR investigation of the equilibrium partitioning of a water-soluble bile salt protein carrier to phospholipid vesicles
Q63339627	NMR investigations of protein-carbohydrate interactions: Studies on the relevance of Trp/Tyr variations in lectin binding sites as deduced from titration microcalorimetry and NMR studies on hevein domains. Determination of the NMR structure of the co
Q30597094	NMR investigations of protein-carbohydrate interactions: studies on the relevance of Trp/Tyr variations in lectin binding sites as deduced from titration microcalorimetry and NMR studies on hevein domains. Determination of the NMR structure of the c
Q52416621	NMR restraint analysis of transforming growth factor alpha: a key component for NMR structure refinement
Q27667126	NMR solution structure of a cyanovirin homolog from wheat head blight fungus
Q27648761	NMR solution structure of the reduced form of thioredoxin 1 from Sacharomyces cerevisiae
Q46489558	NMR structural studies of the Ste11 SAM domain in the dodecyl phosphocholine micelle
Q28492926	NMR structure and binding studies confirm that PA4608 from Pseudomonas aeruginosa is a PilZ domain and a c-di-GMP binding protein
Q46733393	NMR structure and dynamics of human ephrin-B2 ectodomain: the functionally critical C-D and G-H loops are highly dynamic in solution
Q27668187	NMR structure and dynamics of recombinant wild type and mutated jerdostatin, a selective inhibitor of integrin α1β1
Q46177787	NMR structure determination of the conserved hypothetical protein TM1816 from Thermotoga maritima
Q27658972	NMR structure of F-actin-binding domain of Arg/Abl2 from Homo sapiens
Q27643525	NMR structure of YcgL, a conserved protein from Escherichia coli representing the DUF709 family, with a novel alpha/beta/alpha sandwich fold
Q91592049	NMR structure of a full-length single-pass membrane protein NRADD
Q27659504	NMR structure of a phosphatidyl-ethanolamine binding protein from Drosophila
Q27639587	NMR structure of conserved eukaryotic protein ZK652.3 from C. elegans: a ubiquitin-like fold
Q46043067	NMR structure of hypothetical protein MG354 from Mycoplasma genitalium
Q27644198	NMR structure of hypothetical protein TA0938 from Thermoplasma acidophilum
Q27649478	NMR structure of protein Cgl2762 from Corynebacterium glutamicum implicated in DNA transposition reveals a helix-turn-helix motif attached to a flexibly disordered leucine zipper
Q58002361	NMR structure of protein PA2021 from Pseudomonas aeruginosa
Q27655526	NMR structure of protein YvyC fromBacillus subtilisreveals unexpected structural similarity between two PFAM families
Q27643707	NMR structure of protein yjbR from Escherichia coli reveals 'double-wing' DNA binding motif
Q81466373	NMR structure of protein yqbG from Bacillus subtilis reveals a novel alpha-helical protein fold
Q81193213	NMR structure of the 18 kDa protein CC1736 from Caulobacter crescentus identifies a member of the START domain superfamily and suggests residues mediating substrate specificity
Q27639582	NMR structure of the Escherichia coli protein YacG: a novel sequence motif in the zinc-finger family of proteins
Q46295218	NMR structure of the conserved hypothetical protein TM0979 from Thermotoga maritima
Q42676505	NMR structure of the conserved novel-fold protein TA0743 from Thermoplasma acidophilum
Q48007208	NMR structure of the hypothetical protein AQ-1857 encoded by the Y157 gene from Aquifex aeolicus reveals a novel protein fold
Q34315712	NMR structure of the hypothetical protein NMA1147 from Neisseria meningitidis reveals a distinct 5-helix bundle
Q57412389	NMR structure of the hypothetical protein encoded by the YjbJ gene from Escherichia coli
Q27649773	NMR structure of the peptidyl-tRNA hydrolase domain from Pseudomonas syringae expands the structural coverage of the hydrolysis domains of class 1 peptide chain release factors
Q27627408	NMR structures of thioredoxin m from the green alga Chlamydomonas reinhardtii
Q73427987	NMR studies on the flexibility of nucleoside diphosphate kinase
Q31117247	NMR study and molecular dynamics simulations of optimized beta-hairpin fragments of protein G.
Q54613004	NMR study of the reconstitution of the β‐sheet of thioredoxin by fragment complementation
Q92217173	NMR-assisted protein structure prediction with MELDxMD
Q55120792	NMR-based modeling and binding studies of a ternary complex between chicken liver bile acid binding protein and bile acids
Q51765531	NMR-derived solution structure of SUMO from Drosophila melanogaster (dSmt3).
Q27678014	NMR‐based insights into the conformational and interaction properties of Arkadia RING‐H2 E3 Ub ligase
Q62492901	Native and modeled disulfide bonds in proteins: knowledge-based approaches toward structure prediction of disulfide-rich polypeptides
Q77926241	Native and non-native interactions along protein folding and unfolding pathways
Q48385017	Native atomic burials, supplemented by physically motivated hydrogen bond constraints, contain sufficient information to determine the tertiary structure of small globular proteins
Q37431107	Native cysteine residues are dispensable for the structure and function of all five yeast mitotic septins
Q50970471	Native fold and docking pose discrimination by the same residue-based scoring function.
Q47881405	Native secondary structure topology has near minimum contact energy among all possible geometrically constrained topologies
Q47771261	Native state dynamics and mechanical properties of human topoisomerase I within a structure-based coarse-grained model
Q82414680	Native-specific stabilization of flavodoxin by the FMN cofactor: structural and thermodynamical explanation
Q79319223	Natively unfolded C-terminal domain of caldesmon remains substantially unstructured after the effective binding to calmodulin
Q36313231	Natively unfolded regions of the vertebrate fibrinogen molecule
Q74721824	Natural coordinate representation for the protein backbone structure
Q30855071	Natural history of the E1-like superfamily: implication for adenylation, sulfur transfer, and ubiquitin conjugation
Q91880639	Navigating within thiamine diphosphate-dependent decarboxylases: Sequences, structures, functional positions, and binding sites
Q42643521	NdPASA: a novel pairwise protein sequence alignment algorithm that incorporates neighbor-dependent amino acid propensities
Q82548716	Nearest-neighbor effects and structural preferences in dipeptides are a function of the electronic properties of amino acid side-chains
Q81544585	Negative modulation of signal transduction via interleukin splice variation
Q91746091	NetSurfP-2.0: Improved prediction of protein structural features by integrated deep learning
Q40207279	Network mapping among the functional domains of Chikungunya virus nonstructural proteins
Q51538130	Neural network-based prediction of mutation-induced protein stability changes in Staphylococcal nuclease at 20 residue positions
Q31138210	Neutralization of NGF-TrkA receptor interaction by the novel antagonistic anti-TrkA monoclonal antibody MNAC13: a structural insight.
Q71074628	Neutron scattering redux?
Q38852142	Neutron scattering shows a droplet of oleic acid at the center of the BAMLET complex
Q96233499	New Facets of Larger Nest Motifs in Proteins
Q39114594	New additions to the ClusPro server motivated by CAPRI.
Q34792053	New benchmark metrics for protein‐protein docking methods
Q30362203	New classification of supersecondary structures of sandwich-like proteins uncovers strict patterns of strand assemblage.
Q30386087	New computational method for prediction of interacting protein loop regions.
Q27649819	New crystal structures of ColE1 Rom and variants resulting from mutation of a surface exposed residue: Implications for RNA-recognition
Q40256442	New encouraging developments in contact prediction: Assessment of the CASP11 results
Q41615834	New features and enhancements in the X-PLOR computer program
Q77771911	New general approach for determining the solution structure of a ligand bound weakly to a receptor: structure of a fibrinogen Aalpha-like peptide bound to thrombin (S195A) obtained using NOE distance constraints and an ECEPP/3 flexible docking progr
Q39686913	New hypotheses about the structure-function of proprotein convertase subtilisin/kexin type 9: analysis of the epidermal growth factor-like repeat A docking site using WaterMap
Q36342306	New insight into long-range nonadditivity within protein double-mutant cycles
Q53323410	New insight into the architecture of oxy-anion pocket in unliganded conformation of GAT domains: A MD-simulation study.
Q79184908	New insights into DHFR interactions: analysis of Pneumocystis carinii and mouse DHFR complexes with NADPH and two highly potent 5-(omega-carboxy(alkyloxy) trimethoprim derivatives reveals conformational correlations with activity and novel parallel
Q33834449	New insights into the GABA(A) receptor structure and orthosteric ligand binding: receptor modeling guided by experimental data.
Q46886474	New insights into the half‐of‐the‐sites reactivity of human aldehyde dehydrogenase 1A1
Q74615893	New insights into the mechanism of protein-protein association
Q61388013	New insights into the molecular basis of lectin-carbohydrate interactions: A calorimetric and structural study of the association of hevein to oligomers of N-acetylglucosamine
Q38341129	New insights into the molecular basis of lectin-carbohydrate interactions: a calorimetric and structural study of the association of hevein to oligomers of N-acetylglucosamine
Q42637082	New insights of membrane environment effects on MscL channel mechanics from theoretical approaches.
Q52070754	New method for accurate prediction of solvent accessibility from protein sequence
Q30350697	New method for protein secondary structure assignment based on a simple topological descriptor.
Q41665041	New methods for accurate prediction of protein secondary structure
Q27684162	New molecular interaction of IIA(Ntr) and HPr from Burkholderia pseudomallei identified by X-ray crystallography and docking studies
Q28369348	New sequence motifs in flavoproteins: evidence for common ancestry and tools to predict structure
Q74452350	New structural insights into the refolding of ribonuclease T1 as seen by time-resolved Fourier-transform infrared spectroscopy
Q30363495	New tools and expanded data analysis capabilities at the Protein Structure Prediction Center
Q33587709	Nitric oxide conduction by the brain aquaporin AQP4.
Q27749026	Nitric oxide myoglobin: Crystal structure and analysis of ligand geometry
Q71705233	No crystals no grant
Q27621099	Non-Boltzmann thermodynamic integration (NBTI) for macromolecular systems: relative free energy of binding of trypsin to benzamidine and benzylamine
Q58484036	Non-heme iron through the three domains of life
Q53657663	Non-interacting surface solvation and dynamics in protein-protein interactions
Q48009975	Non-intertwined binary patterns of hydrophobic/nonhydrophobic amino acids are considerably better markers of regular secondary structures than nonconstrained patterns
Q43494033	Non-native alpha-helix formation is not necessary for folding of lipocalin: comparison of burst-phase folding between tear lipocalin and beta-lactoglobulin
Q30165223	Non-native interactions, effective contact order, and protein folding: a mutational investigation with the energetically frustrated hydrophobic model
Q47626865	Non-randomness in side-chain packing: the distribution of interplanar angles
Q57893163	Non-randomness in side-chain packing: the distribution of interplanar angles
Q41820978	Nonadditive effects of mixed crowding on protein stability
Q30332169	Nonatomic solvent-driven Voronoi tessellation of proteins: an open tool to analyze protein folds.
Q27665113	Noncellulosomal cohesin from the hyperthermophilic archaeon Archaeoglobus fulgidus
Q56794559	Noncovalent interaction energies in covalent complexes: TEM-1 ?-lactamase and ?-lactams
Q27638114	Noncovalent interaction energies in covalent complexes: TEM-1 beta-lactamase and beta-lactams
Q52012574	Nonequilibrium, multiple-timescale simulations of ligand-receptor interactions in structured protein systems
Q36172642	Nonlinearities in protein space limit the utility of informatics in protein biophysics
Q30372401	Nonrandom distribution of intramolecular contacts in native single-domain proteins.
Q33231136	Nontoxic crystal protein from Bacillus thuringiensis demonstrates a remarkable structural similarity to beta-pore-forming toxins
Q45134647	Noonan syndrome type I with PTPN11 3 bp deletion: structure-function implications.
Q41219658	Normal mode analysis of human lysozyme: study of the relative motion of the two domains and characterization of the harmonic motion
Q28220822	Normal mode analysis of macromolecular motions in a database framework: developing mode concentration as a useful classifying statistic
Q72890887	Normal mode analysis of mouse epidermal growth factor: characterization of the harmonic motion
Q68701376	Normal modes of vibration in bovine pancreatic trypsin inhibitor and its mechanical property
Q33346847	Normal-mode-based modeling of allosteric couplings that underlie cyclic conformational transition in F(1) ATPase
Q38288438	Norovirus RNA-dependent RNA polymerase: A computational study of metal-binding preferences
Q27694651	Novel RNA recognition motif domain in the cytoplasmic polyadenylation element binding protein 3
Q30357297	Novel approach for alpha-helical topology prediction in globular proteins: generation of interhelical restraints.
Q44784457	Novel approaches for modeling of the A1 adenosine receptor and its agonist binding site
Q27648765	Novel cation-pi interaction revealed by crystal structure of thermoalkalophilic lipase
Q28296637	Novel conserved hydrolase domain in the CLCA family of alleged calcium-activated chloride channels
Q34082509	Novel high-affinity binders of human interferon gamma derived from albumin-binding domain of protein G.
Q46985514	Novel insights on the mechanism of action of alpha-amylase inhibitors from the plant defensin family
Q70628287	Novel mechanism-based substrates of dihydrofolate reductase and the thermodynamics of ligand binding: a comparison of theory and experiment for 8-methylpterin and 6,8-dimethylpterin
Q48193128	Novel modulation factor quantifies the role of water molecules in protein interactions
Q90071656	Novel phosphorylation-dependent regulation in an unstructured protein
Q30389896	Novel proteases from the genome of the carnivorous plant Drosera capensis: Structural prediction and comparative analysis
Q27642859	Novel protein and Mg2+ configurations in the Mg2+GDP complex of the SRP GTPase ffh
Q91336731	Novel sampling strategies and a coarse-grained score function for docking homomers, flexible heteromers, and oligosaccharides using Rosetta in CAPRI rounds 37-45
Q53634234	Novel scoring function for modeling structures of oligomers of transmembrane alpha-helices
Q81478489	Novel statistical-thermodynamic methods to predict protein-ligand binding positions using probability distribution functions
Q30163968	Novel structure and nucleotide binding properties of HI1480 from Haemophilus influenzae: a protein with no known sequence homologues.
Q30336224	Novel use of a genetic algorithm for protein structure prediction: searching template and sequence alignment space.
Q34497427	Novel, structure-based mechanism for uridylylation of the genome-linked peptide (VPg) of picornaviruses
Q47715131	NrdH-redoxin of Corynebacterium ammoniagenes forms a domain-swapped dimer
Q91793612	Nuclear magnetic resonance solution structure of Pisum sativum defensin 2 provides evidence for the presence of hydrophobic surface-clusters
Q46871543	Nucleation‐based prediction of the protein folding rate and its correlation with the folding nucleus size
Q27627766	Nucleoside binding site of herpes simplex type 1 thymidine kinase analyzed by X-ray crystallography
Q57077664	Nucleotide recognition by the initiation factor aIF5B: Free energy simulations of a neoclassical GTPase
Q46155035	Nucleotide-dependence of G-actin conformation from multiple molecular dynamics simulations and observation of a putatively polymerization-competent superclosed state
Q86743397	Nucleotide-dependent structural fluctuations and regulation of microtubule-binding affinity of KIF1A
Q30429648	Numerical criteria for the evaluation of ab initio predictions of protein structure.
Q96163465	Numerous severely twisted N-acetylglucosamine conformations found in the protein databank
Q38328181	O-raffinose crosslinked hemoglobin lacks site-specific chemistry in the central cavity: structural and functional consequences of beta93Cys modification
Q52948319	Observation of residual dipolar couplings in short peptides
Q56985409	Observing the osmophobic effect in action at the single molecule level
Q47296648	Octanol-water partition of nonzwitterionic peptides: predictive power of a molecular size-based model
Q79757159	Old fold in a new X-ray diffraction dataset? Low-resolution molecular replacement using representative structural templates can provide phase information
Q95305906	Oleg borisovich ptitsyn: july 18, 1929-march 22, 1999
Q81211360	Oligomerization states of Bowman-Birk inhibitor by atomic force microscopy and computational approaches
Q30430086	Oligopeptidase B: Cloning and probing stability under nonequilibrium conditions
Q34170542	Oligopeptide biases in protein sequences and their use in predicting protein coding regions in nucleotide sequences
Q80474169	On defining the dynamics of hydrophobic patches on protein surfaces
Q30376364	On interpretation of protein X-ray structures: Planarity of the peptide unit.
Q93074531	On predicting foldability of a protein from its sequence
Q30402886	On the Relationship between Residue Structural Environment and Sequence Conservation in Proteins
Q84309305	On the accuracy of inferring energetic coupling between distant sites in protein families from evolutionary imprints: illustrations using lattice model
Q72074160	On the calculation of pKas in proteins
Q52206949	On the convergence of the conformational coordinates basis set obtained by the essential dynamics analysis of proteins' molecular dynamics simulations
Q52078678	On the design and analysis of protein folding potentials
Q35353400	On the development of protein pKa calculation algorithms.
Q112638612	On the diversity of F₄₂₀ -dependent oxidoreductases: A sequence- and structure-based classification
Q35013835	On the diversity of physicochemical environments experienced by identical ligands in binding pockets of unrelated proteins
Q47589359	On the effect of mutations in bovine or camel chymosin on the thermodynamics of binding κ-caseins
Q45001065	On the evolutionary origin of the chaperonins.
Q30341348	On the functional significance of electron density protein structure alignments.
Q41823477	On the helix sense of gramicidin A single channels
Q60214202	On the mechanism of human stefin B folding: I. Comparison to homologous stefin A. Influence of pH and trifluoroethanol on the fast and slow folding phases
Q60214206	On the mechanism of human stefin B folding: II. Folding from GuHCl unfolded, TFE denatured, acid denatured, and acid intermediate states
Q30393176	On the mechanism of protein fold‐switching by a molecular sensor
Q50522986	On the molecular structure of human neuroserpin polymers
Q52465385	On the multiple-minima problem in the conformational analysis of polypeptides. V. Application of the self-consistent electrostatic field and the electrostatically driven monte carlo methods to bovine pancreatic trypsin inhibitor
Q67656994	On the nature of antibody combining sites: Unusual structural features that may confer on these sites an enhanced capacity for binding ligands
Q34494450	On the nature of cavities on protein surfaces: application to the identification of drug-binding sites
Q43180953	On the orientation of the catalytic dyad in aspartic proteases
Q37399660	On the origin of the catalytic power of carboxypeptidase A and other metalloenzymes
Q30176762	On the origin of the cooperativity of protein folding: implications from model simulations
Q42675018	On the pH-optimum of activity and stability of proteins
Q92737932	On the presence of short-range periodicities in protein structures that are not related to established secondary structure elements
Q62141729	On the reaction mechanism of class Pi glutathione S-transferase
Q51775528	On the relation between residue flexibility and local solvent accessibility in proteins
Q28391996	On the relationship between NMR-derived amide order parameters and protein backbone entropy changes
Q30367569	On the relationship between the protein structure and protein dynamics.
Q30427194	On the relationship between the sequence conservation and the packing density profiles of the protein complexes
Q36809892	On the sensitivity of MD trajectories to changes in water-protein interaction parameters: the potato carboxypeptidase inhibitor in water as a test case for the GROMOS force field
Q44620087	On the stoichiometry of Deinococcus radiodurans Dps-1 binding to duplex DNA.
Q91163228	On the structure and function of Escherichia coli YjhC: An oxidoreductase involved in bacterial sialic acid metabolism
Q74177410	On the unfolding of alpha-lytic protease and the role of the pro region
Q51508072	On the use of distance constraints in protein–protein docking computations
Q47586265	On the use of structural templates for high-resolution docking
Q30352480	One contact for every twelve residues allows robust and accurate topology-level protein structure modeling
Q45288452	One gene, two diseases and three conformations: molecular dynamics simulations of mutants of human prion protein at room temperature and elevated temperatures
Q82665082	One‐bond and two‐bond j couplings help annotate protein secondary‐structure motifs: J‐coupling indexing applied to human endoplasmic reticulum protein ERp18
Q38801229	Open and compressed conformations of Francisella tularensis ClpP.
Q46335123	Opening of the ADP-bound active site in the ABC transporter ATPase dimer: evidence for a constant contact, alternating sites model for the catalytic cycle.
Q50312505	Operational definition of intrinsically unstructured protein sequences based on susceptibility to the 20S proteasome.
Q44398469	Operons and the effect of genome redundancy in deciphering functional relationships using phylogenetic profiles
Q35450179	Opposing orientations of the anti-psychotic drug trifluoperazine selected by alternate conformations of M144 in calmodulin
Q31165105	Optimal data collection for correlated mutation analysis
Q47604362	Optimal design of protein docking potentials: efficiency and limitations
Q46609131	Optimal docking area: a new method for predicting protein-protein interaction sites
Q71537057	Optimal local propensities for model proteins
Q52114194	Optimal potentials for predicting inter-helical packing in transmembrane proteins.
Q43284323	Optimal protein-RNA area, OPRA: a propensity-based method to identify RNA-binding sites on proteins
Q74449574	Optimally informative backbone structural propensities in proteins
Q42601395	Optimization of 3D Poisson-Nernst-Planck model for fast evaluation of diverse protein channels
Q52072060	Optimization of a new score function for the detection of remote homologs
Q74721964	Optimization of a new score function for the generation of accurate alignments
Q34625066	Optimization of molecular docking scores with support vector rank regression
Q46809714	Optimization of multiple-sequence alignment based on multiple-structure alignment
Q51682700	Optimization of pyDock for the new CAPRI challenges: Docking of homology-based models, domain-domain assembly and protein-RNA binding
Q57135150	Optimization of solvation models for predicting the structure of surface loops in proteins
Q41334195	Optimization of the design and preparation of nanoscale phospholipid bilayers for its application to solution NMR.
Q34357490	Optimized E. coli expression strain LOBSTR eliminates common contaminants from His-tag purification
Q30371877	Optimized distance-dependent atom-pair-based potential DOOP for protein structure prediction.
Q51604620	Optimized grid‐based protein–protein docking as a global search tool followed by incorporating experimentally derivable restraints
Q73403630	Optimized representations and maximal information in proteins
Q51624323	Optimizing pKa computation in proteins with pH adapted conformations
Q52005571	Optimizing physical energy functions for protein folding
Q50892827	Optimizing the affinity and specificity of ligand binding with the inclusion of solvation effect
Q52064388	Optimizing the hydrogen-bond network in Poisson-Boltzmann equation-based pK(a) calculations.
Q37369361	Order propensity of an intrinsically disordered protein, the cyclin-dependent-kinase inhibitor Sic1
Q41870328	Order within disorder: aggrecan chondroitin sulphate-attachment region provides new structural insights into protein sequences classified as disordered
Q31142431	Ordered conformational change in the protein backbone: prediction of conformationally variable positions from sequence and low-resolution structural data
Q57348546	Ordering of adsorbed proteins
Q45777079	Organization of turnip yellow mosaic virus investigated by neutron small angle scattering at 80 K: an intermediate state preceding decapsidation of the virion?
Q46595884	Orientation and rotational dynamics of spin-labeled phalloidin bound to actin in muscle fibers
Q42160644	Orientational distributions of contact clusters in proteins closely resemble those of an icosahedron
Q46268512	Orientational sampling and rigid-body minimization in molecular docking
Q42600798	Origin of functional diversity among tetrameric voltage-gated channels.
Q81282353	Origin of the sequence-dependent polyproline II structure in unfolded peptides
Q42686721	Origins of protein denatured state compactness and hydrophobic clustering in aqueous urea: inferences from nonpolar potentials of mean force
Q46953779	Osmolyte effect on the stability and folding of a hyperthermophilic protein
Q46924080	Osmolyte-induced protein folding free energy changes
Q27652430	Outer membrane cytochrome c, OmcF, from Geobacter sulfurreducens: high structural similarity to an algal cytochrome c6
Q36297691	Overcoming sequence misalignments with weighted structural superposition
Q71565971	Overexpression of Bacillus subtilis phosphoribosylpyrophosphate synthetase and crystallization and preliminary X-ray characterization of the free enzyme and its substrate-effector complexes
Q46853497	Overexpression, physicochemical characterization, and modeling of a hyperthermophilic pyrococcus furiosus type 2 IPP isomerase.
Q44165216	Overlapping binding sites for trypsin and papain on a Kunitz-type proteinase inhibitor from Prosopis juliflora.
Q44252098	Overproduction, crystallization, and preliminary X-ray diffraction studies of the major cold shock protein from Bacillus subtilis, CspB.
Q91217872	Oxidase or peptidase? A computational insight into a putative aflatoxin oxidase from Armillariella tabescens
Q92331319	Oxidation-induced destabilization of the fibrinogen αC-domain dimer investigated by molecular dynamics simulations
Q80238521	Oxygen affinity controlled by dynamical distal conformations: the soybean leghemoglobin and the Paramecium caudatum hemoglobin cases
Q56272088	Oxygen and proton pathways in cytochrome c oxidase
Q71671446	Oxygen binding by single crystals of hemoglobin: the problem of cooperativity and inequivalence of alpha and beta subunits
Q35045263	PAIRpred: partner-specific prediction of interacting residues from sequence and structure
Q101041487	PDB-Tools Web: A user-friendly interface for the manipulation of PDB files
Q46988348	PDB‐scale analysis of known and putative ligand‐binding sites with structural sketches
Q27972551	PFP: Automated prediction of gene ontology functional annotations with confidence scores using protein sequence data
Q42149736	PIE-efficient filters and coarse grained potentials for unbound protein-protein docking
Q30359869	PIER: protein interface recognition for structural proteomics.
Q46857534	PII structure in the model peptides for unfolded proteins: studies on ubiquitin fragments and several alanine-rich peptides containing QQQ, SSS, FFF, and VVV.
Q41872855	PIK3CA somatic mutations in breast cancer: Mechanistic insights from Langevin dynamics simulations
Q51140851	PIPER: an FFT-based protein docking program with pairwise potentials
Q30394800	PKB: a program system and data base for analysis of protein structure
Q58091494	PLUG (Pruning of Local Unrealistic Geometries) removes restrictions on biophysical modeling for protein design
Q57953054	PPRODO: Prediction of protein domain boundaries using neural networks
Q42654619	PRED-CLASS: cascading neural networks for generalized protein classification and genome-wide applications
Q31107931	PREDICT modeling and in-silico screening for G-protein coupled receptors.
Q33653515	PRIMO/PRIMONA: a coarse-grained model for proteins and nucleic acids that preserves near-atomistic accuracy
Q51119552	PRIMSIPLR: prediction of inner-membrane situated pore-lining residues for alpha-helical transmembrane proteins
Q51373396	PRL-Dock: protein-ligand docking based on hydrogen bond matching and probabilistic relaxation labeling.
Q51293025	PSI-DOCK: towards highly efficient and accurate flexible ligand docking.
Q38392351	PSLDoc: Protein subcellular localization prediction based on gapped-dipeptides and probabilistic latent semantic analysis
Q30406911	PackHelix: A tool for helix‐sheet packing during protein structure prediction
Q70628280	Packing and recognition of protein structural elements: a new approach applied to the 4-helix bundle of myohemerythrin
Q52348350	Packing constraints of hydrophobic side chains in (alpha/beta)8 barrels
Q52243187	Packing forces in nine crystal forms of cutinase
Q33599950	Packing interface energetics in different crystal forms of the λ Cro dimer
Q27644869	Pactolus I-domain: functional switching of the Rossmann fold
Q47658298	Pairwise contact energy statistical potentials can help to find probability of point mutations.
Q41826221	Pan1 is an intrinsically disordered protein with homotypic interactions
Q57977961	Pancreatic spasmolytic polypeptide: Crystallization, circular dichroism analysis, and preliminary X-ray diffraction studies
Q31113034	Parallel tempering molecular dynamics folding simulation of a signal peptide in explicit water
Q52012571	Parallel tempering simulations of HP-36.
Q52253536	Paramagnetic relaxation as a tool for solution structure determination: Clostridium pasteurianum ferredoxin as an example
Q58484081	Paramagnetic relaxation as a tool for solution structure determination:Clostridium pasteurianum ferredoxin as an example
Q70980733	Parametric sensitivity analysis of avian pancreatic polypeptide (APP)
Q28239434	Parser for protein folding units
Q47430859	Partial atomic charges of amino acids in proteins
Q46615228	Partial destabilization of native structure by a combination of heat and denaturant facilitates cold denaturation in a hyperthermophile protein.
Q30380377	Partial unfolding and refolding for structure refinement: A unified approach of geometric simulations and molecular dynamics.
Q30344054	Partition of protein solvation into group contributions from molecular dynamics simulations.
Q60431912	Partner‐specific Prediction of RNA‐binding Residues in Proteins: A Critical Assessment
Q56970691	Pathway heterogeneity in protein folding
Q38348081	Pattern descriptors and the unidentified reading frame 6 human mtDNA dinucleotide-binding site
Q73365498	Patterns in ionizable side chain interactions in protein structures
Q30432219	Patterns of protein-fold usage in eight microbial genomes: a comprehensive structural census
Q45039434	Patterns of retinal light absorption related to retinitis pigmentosa mutants from in silico model structures of rhodopsin
Q30426650	Patterns, structures, and amino acid frequencies in structural building blocks, a protein secondary structure classification scheme
Q42985865	Pentacoordinated phosphorus revisited by high-level QM/MM calculations.
Q46580529	Pepsinogen-like activation intermediate of plasmepsin II revealed by molecular dynamics analysis
Q98937816	PeptiDesCalculator : Software for Computation of Peptide Descriptors. Definition, Implementation and Case Studies for 9 Bioactivity Endpoints
Q68786417	Peptide and ester synthesis in organic solvents catalyzed by seryl proteases linked to alumina
Q47427287	Peptide binding to the PDZ3 domain by conformational selection
Q46815490	Peptide fragment studies on the folding elements of dihydrofolate reductase from Escherichia coli
Q45199812	Peptide models XLV: conformational properties of N-formyl-L-methioninamide and its relevance to methionine in proteins
Q69364371	Peptide sequencing and site-directed mutagenesis identify tyrosine-319 as the active site tyrosine of Escherichia coli DNA topoisomerase I
Q68457829	Peptide synthesis catalyzed by polyethylene glycol-modified chymotrypsin in organic solvents
Q30423608	Perfect temperature for protein structure prediction and folding.
Q91163198	Performance and enhancement of the LZerD protein assembly pipeline in CAPRI 38-46
Q50110817	Performance evaluation of a new algorithm for the detection of remote homologs with sequence comparison
Q72589783	Performance evaluation of amino acid substitution matrices
Q96131812	Performance of Human and Server Prediction in CAPRI rounds 38-45
Q48947966	Performance of MDockPP in CAPRI rounds 28-29 and 31-35 including the prediction of water-mediated interactions
Q50562538	Performance of ZDOCK and IRAD in CAPRI rounds 28-34.
Q93026635	Performance of ZDOCK and IRAD in CAPRI rounds 39-45
Q41981451	Performance of ZDOCK and ZRANK in CAPRI rounds 13-19.
Q37684662	Performance of ZDOCK in CAPRI rounds 20-26.
Q30379331	Performance of the Pro-sp3-TASSER server in CASP8
Q58489123	Performance of the first protein docking server ClusPro in CAPRI rounds 3-5
Q51922354	Periodic distributions of hydrophobic amino acids allows the definition of fundamental building blocks to align distantly related proteins
Q58048764	Permeation of water through the KcsA K+channel
Q103007520	Persistent homology and application on residues 1-28 of amyloid beta peptide
Q42644226	Perspectives and expectations in structural bioinformatics of metalloproteins
Q27732119	Perturbation of Trp 138 in T4 lysozyme by mutations at Gln 105 used to correlate changes in structure, stability, solvation, and spectroscopic properties
Q73083596	Perturbation of conformational dynamics, enzymatic activity, and thermostability of beta-glycosidase from archaeon Sulfolobus solfataricus by pH and sodium dodecyl sulfate detergent
Q103048188	Perturbing the energy landscape for improved packing during computational protein design
Q48767965	Peter Andrew Kollman
Q48623700	Pex, analytical tools for PDB files. I. GF-Pex: basic file to describe a protein
Q52068718	Pex, analytical tools for PDB files. II. H-Pex: noncanonical H-bonds in alpha-helices
Q44898259	Pex5p binding affinities for canonical and noncanonical PTS1 peptides.
Q29614439	Pfam: a comprehensive database of protein domain families based on seed alignments
Q92445560	Phage display derived therapeutic antibodies have enriched aliphatic content: Insights for developability issues
Q30875156	Phage-display and correlated mutations identify an essential region of subdomain 1C involved in homodimerization of Escherichia coli FtsA.
Q44379444	Pharmacophore-based molecular docking to account for ligand flexibility
Q27729292	Phe-46(CD4) orients the distal histidine for hydrogen bonding to bound ligands in sperm whale myoglobin
Q43014614	Phenomenological similarities between protein denaturation and small-molecule dissolution: Insights into the mechanism driving the thermal resistance of globular proteins
Q38324605	Phenotype analysis using network motifs derived from changes in regulatory network dynamics
Q27690019	Phenotypic comparisons of consensus variants versus laboratory resurrections of Precambrian proteins
Q34370332	PhosphaBase: an ontology-driven database resource for protein phosphatases.
Q37229460	Phospholipase A2 at the bilayer interface
Q51522059	Phosphorylation alters backbone conformational preferences of serine and threonine peptides.
Q46560912	Phosphorylation of either Ser16 or Thr30 does not disrupt the structure of the Itch E3 ubiquitin ligase third WW domain
Q83949081	Phosphorylation-induced transient intrinsic structure in the kinase-inducible domain of CREB facilitates its recognition by the KIX domain of CBP
Q38348076	Photochemical crosslinking of bacteriophage T4 single-stranded DNA-binding protein (gp32) to oligo-p(dT)8: identification of phenylalanine-183 as the site of crosslinking
Q46375493	Photoinduced fibrils formation of chicken egg white lysozyme under native conditions
Q48414049	Phylogenetic analysis of haloalkane dehalogenases
Q52050100	Phylogenetic information improves homology detection
Q48064976	Phylogenetic occurrence of coiled coil proteins: implications for tissue structure in metazoa via a coiled coil tissue matrix
Q87910630	Phylogenetic spread of sequence data affects fitness of SOD1 consensus enzymes: Insights from sequence statistics and structural analyses
Q92585857	Phylogenetic spread of sequence data affects fitness of consensus enzymes: Insights from triosephosphate isomerase
Q48213548	Physical interaction between the strawberry allergen Fra a 1 and an associated partner FaAP: Interaction of Fra a 1 proteins and FaAP.
Q68051375	Physical reasons for secondary structure stability: alpha-helices in short peptides
Q30342098	Physical scoring function based on AMBER force field and Poisson-Boltzmann implicit solvent for protein structure prediction.
Q39346444	Physicochemical descriptors to discriminate protein-protein interactions in permanent and transient complexes selected by means of machine learning algorithms
Q57021685	Physicochemical explanation of peptide binding to HLA-A*0201 major histocompatibility complex: A three-dimensional quantitative structure-activity relationship study
Q56893550	Physics-based enzyme design: predicting binding affinity and catalytic activity
Q30431472	Physics‐based protein structure refinement through multiple molecular dynamics trajectories and structure averaging
Q52261424	Picosecond dynamical changes on denaturation of yeast phosphoglycerate kinase revealed by quasielastic neutron scattering
Q44706729	Picosecond dynamics of the glutamate receptor in response to agonist-induced vibrational excitation
Q52395599	Picosecond timescale rigid-helix and side-chain motions in deoxymyoglobin
Q38565768	Pitch diversity in alpha-helical coiled coils
Q27657492	Plasmodium falciparumacyl carrier protein crystal structures in disulfide-linked and reduced states and their prevalence during blood stage growth
Q27666626	Plastic adaptation toward mutations in proteins: structural comparison of thymidylate synthases
Q27621911	Plasticity and steric strain in a parallel beta-helix: rational mutations in the P22 tailspike protein
Q72635012	Polar and nonpolar atomic environments in the protein core: implications for folding and binding
Q57000556	Polar hydrogen positions in proteins: Empirical energy placement and neutron diffraction comparison
Q46379655	Poly-(L-alanine) expansions form core beta-sheets that nucleate amyloid assembly.
Q38956652	Polyanion binding accelerates the formation of stable and low-toxic aggregates of ALS-linked SOD1 mutant A4V.
Q84084543	Polyglutamine fibrils are formed using a simple designed beta-hairpin model
Q81094719	Polyglutamine homopolymers having 8-45 residues form slablike beta-crystallite assemblies
Q61797583	Polyglutamine repeats and β-helix structure: Molecular dynamics study
Q74015806	Polymer principles of protein calorimetric two-state cooperativity
Q58663907	Polymer principles of protein calorimetric two‐state cooperativity
Q47715263	Polyproline II helix is the preferred conformation for unfolded polyalanine in water
Q30453036	Polyproline, beta-turn helices. Novel secondary structures proposed for the tandem repeats within rhodopsin, synaptophysin, synexin, gliadin, RNA polymerase II, hordein, and gluten
Q73713059	Population analyses of kinetic partitioning in protein folding
Q41906900	Population shift of binding pocket size and dynamic correlation analysis shed new light on the anticooperative mechanism of PII protein
Q77603390	Populations of hydrophobic amino acids within protein globular domains: identification of conserved "topohydrophobic" positions
Q30160412	Porcine beta-lactoglobulin chemical unfolding: identification of a non-native alpha-helical intermediate
Q30364677	Position-resolved free energy of solvation for amino acids in lipid membranes from molecular dynamics simulations.
Q30426168	Positioning hydrogen atoms by optimizing hydrogen-bond networks in protein structures
Q30330111	Positioning of anchor groups in protein loop prediction: the importance of solvent accessibility and secondary structure elements.
Q83782515	Possible ligand release pathway of dipeptidyl peptidase IV investigated by molecular dynamics simulations
Q44496112	Possible locally driven folding pathways of TC5b, a 20-residue protein
Q38291985	Potential DNA binding and nuclease functions of ComEC domains characterized in silico
Q27664233	Potential anti-bacterial drug target: structural characterization of 3,4-dihydroxy-2-butanone-4-phosphate synthase from Salmonella typhimurium LT2
Q31101722	Potential folding-function interrelationship in proteins
Q30355042	Potential for assessing quality of protein structure based on contact number prediction.
Q77538018	Potential of mean force for protein-protein interaction studies
Q74177429	Practical limits of function prediction
Q92806794	Pre- and post-docking sampling of conformational changes using ClustENM and HADDOCK for protein-protein and protein-DNA systems
Q35212044	Prechemistry versus preorganization in DNA replication fidelity
Q68697902	Predicted calmodulin-binding sequence in the gamma subunit of phosphorylase b kinase
Q30388330	Predicted residue-residue contacts can help the scoring of 3D models
Q30341638	Predicted role for the archease protein family based on structural and sequence analysis of TM1083 and MTH1598, two proteins structurally characterized through structural genomics efforts.
Q72154705	Predicted secondary and supersecondary structure for the serine-threonine-specific protein phosphatase family
Q101219690	Predicted structural differences of four fertility-related Y-chromosome proteins in Macaca mulatta, M. fascicularis, and their Indochinese hybrids
Q73256232	Predicted structure and fold recognition for the glutamyl tRNA reductase family of proteins
Q34975607	Predicted structures of agonist and antagonist bound complexes of adenosine A3 receptor
Q46019611	Predicted three-dimensional structure of the protease inhibitor domain of the Alzheimer's disease beta-amyloid precursor.
Q41557386	Predicting Ca2+‐binding sites using refined carbon clusters
Q30360181	Predicting DNA-binding amino acid residues from electrostatic stabilization upon mutation to Asp/Glu and evolutionary conservation.
Q51936758	Predicting G-protein coupled receptors-G-protein coupling specificity based on autocross-covariance transform
Q30344115	Predicting absolute contact numbers of native protein structure from amino acid sequence.
Q68704284	Predicting antibody hypervariable loop conformations. II: Minimization and molecular dynamics studies of MCPC603 from many randomly generated loop conformations
Q38764353	Predicting binding modes of reversible peptide-based inhibitors of falcipain-2 consistent with structure-activity relationships.
Q30353913	Predicting calcium-binding sites in proteins - a graph theory and geometry approach.
Q103007988	Predicting cryptic ligand binding sites based on normal modes guided conformational sampling
Q30359722	Predicting disulfide connectivity patterns.
Q35534782	Predicting drug resistance of the HIV-1 protease using molecular interaction energy components
Q43872323	Predicting enzymatic function from global binding site descriptors
Q51905720	Predicting experimental properties of integral membrane proteins by a naive Bayes approach
Q35541836	Predicting extreme pKa shifts in staphylococcal nuclease mutants with constant pH molecular dynamics
Q35624629	Predicting flexible loop regions that interact with ligands: the challenge of accurate scoring
Q43480874	Predicting functional residues in Plasmodium falciparum plasmepsins by combining sequence and structural analysis with molecular dynamics simulations.
Q52261428	Predicting helical segments in proteins by a helix-coil transition theory with parameters derived from a structural database of proteins
Q30369612	Predicting helix orientation for coiled-coil dimers
Q34379398	Predicting human immunodeficiency virus protease cleavage sites in proteins by a discriminant function method
Q44593620	Predicting interactions of winged-helix transcription factors with DNA.
Q79210022	Predicting interresidue contacts using templates and pathways
Q47422786	Predicting intrinsic disorder from amino acid sequence
Q44372128	Predicting kinetic constants of protein-protein interactions based on structural properties.
Q30406906	Predicting large-scale conformational changes in proteins using energy-weighted normal modes.
Q52372459	Predicting molecular interactions and inducible complementarity: fragment docking of Fab-peptide complexes.
Q52046754	Predicting novel protein folds by using FRAGFOLD.
Q30409524	Predicting nucleic acid binding interfaces from structural models of proteins
Q42985707	Predicting order of conformational changes during protein conformational transitions using an interpolated elastic network model
Q47236441	Predicting peptide binding to MHC pockets via molecular modeling, implicit solvation, and global optimization
Q52181475	Predicting peptides that bind to MHC molecules using supervised learning of hidden Markov models
Q30424729	Predicting permanent and transient protein–protein interfaces
Q34491235	Predicting protease types by hybridizing gene ontology and pseudo amino acid composition
Q51773361	Predicting protein complex geometries with a neural network
Q45949461	Predicting protein conformational changes for unbound and homology docking: learning from intrinsic and induced flexibility.
Q33278353	Predicting protein domain interactions from coevolution of conserved regions
Q30399245	Predicting protein flexibility through the prediction of local structures
Q51645839	Predicting protein folding rate change upon point mutation using residue-level coevolutionary information.
Q45169320	Predicting protein functional sites with phylogenetic motifs
Q46853504	Predicting protein homocysteinylation targets based on dihedral strain energy and pKa of cysteines
Q30366480	Predicting protein interaction interfaces from protein sequences: case studies of subtilisin and phycocyanin.
Q51800509	Predicting protein pK(a) by environment similarity
Q34266160	Predicting protein quaternary structure by pseudo amino acid composition
Q57017390	Predicting protein quaternary structure by pseudo amino acid composition
Q51964764	Predicting protein secondary structure and solvent accessibility with an improved multiple linear regression method
Q30429645	Predicting protein structure using hidden Markov models
Q30323183	Predicting protein structure using only sequence information.
Q33712176	Predicting protein-DNA interactions by full search computational docking
Q42111437	Predicting residue-residue contact maps by a two-layer, integrated neural-network method
Q52306159	Predicting solvent accessibility: higher accuracy using Bayesian statistics and optimized residue substitution classes
Q43686780	Predicting structural effects in HIV-1 protease mutant complexes with flexible ligand docking and protein side-chain optimization
Q42550838	Predicting structurally conserved contacts for homologous proteins using sequence conservation filters
Q42164192	Predicting the disulfide bonding state of cysteines using protein descriptors
Q73134800	Predicting the equilibrium protein folding pathway: structure-based analysis of staphylococcal nuclease
Q51478939	Predicting the functional motions of p97 using symmetric normal modes
Q38612068	Predicting the helix-helix interactions from correlated residue mutations.
Q42153432	Predicting the order in which contacts are broken during single molecule protein stretching experiments
Q46917629	Predicting the redox state and secondary structure of cysteine residues in proteins using NMR chemical shifts
Q30363422	Predicting the side-chain dihedral angle distributions of nonpolar, aromatic, and polar amino acids using hard sphere models.
Q31031926	Predicting the three-dimensional structure of human P-glycoprotein in absence of ATP by computational techniques embodying crosslinking data: insight into the mechanism of ligand migration and binding sites.
Q30159712	Predicting transmembrane beta-barrels and interstrand residue interactions from sequence
Q40175476	Predicting transmembrane helix pair configurations with knowledge-based distance-dependent pair potentials
Q52244712	Prediction and classification of domain structural classes
Q40921775	Prediction and evaluation of side-chain conformations for protein backbone structures
Q51353182	Prediction and evolutionary information analysis of protein solvent accessibility using multiple linear regression
Q51905722	Prediction and scoring of docking poses with pyDock
Q37629422	Prediction and validation of the unexplored RNA-binding protein atlas of the human proteome
Q45964055	Prediction of 3D metal binding sites from translated gene sequences based on remote-homology templates.
Q28274221	Prediction of CASP6 structures using automated Robetta protocols
Q28264124	Prediction of EF-hand calcium-binding proteins and analysis of bacterial EF-hand proteins
Q91460796	Prediction of GABARAP interaction with the GABA type A receptor
Q51903854	Prediction of RNA binding sites in a protein using SVM and PSSM profile.
Q51609595	Prediction of RNA-binding residues in proteins from primary sequence using an enriched random forest model with a novel hybrid feature
Q57979389	Prediction of VH-VL domain orientation for antibody variable domain modeling
Q30339066	Prediction of alpha-turns in proteins using PSI-BLAST profiles and secondary structure information.
Q42426481	Prediction of an HMG-box fold in the C-terminal domain of histone H1: insights into its role in DNA condensation.
Q51980286	Prediction of binding modes for ligands in the cytochromes P450 and other heme-containing proteins.
Q51955731	Prediction of buried helices in multispan alpha helical membrane proteins
Q51935911	Prediction of continuous B-cell epitopes in an antigen using recurrent neural network
Q30330076	Prediction of coordination number and relative solvent accessibility in proteins.
Q59351799	Prediction of cross-clade HIV-1 T-cell epitopes using immunoinformatics analysis
Q31028185	Prediction of deleterious functional effects of amino acid mutations using a library of structure-based function descriptors
Q34272402	Prediction of disordered regions in proteins from position specific score matrices
Q51555186	Prediction of distant residue contacts with the use of evolutionary information.
Q42668404	Prediction of disulfide connectivity from protein sequences
Q90300121	Prediction of folding mechanisms for Ig-like beta sandwich proteins based on inter-residue average distance statistics methods
Q47248696	Prediction of folding pathway and kinetics among plant hemoglobins using an average distance map method.
Q73025077	Prediction of folding rates and transition-state placement from native-state geometry
Q30361364	Prediction of folding transition-state position (betaT) of small, two-state proteins from local secondary structure content.
Q30364784	Prediction of global and local model quality in CASP7 using Pcons and ProQ.
Q45963615	Prediction of global and local model quality in CASP8 using the ModFOLD server.
Q30378304	Prediction of global and local quality of CASP8 models by MULTICOM series.
Q43730210	Prediction of helix-helix contacts and interacting helices in polytopic membrane proteins using neural networks
Q45946283	Prediction of homologous protein structures based on conformational searches and energetics.
Q30387414	Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment
Q46733397	Prediction of interaction sites from apo 3D structures when the holo conformation is different
Q33221093	Prediction of interface residues in protein-protein complexes by a consensus neural network method: test against NMR data
Q45184365	Prediction of interfaces for oligomerizations of G-protein coupled receptors.
Q91821907	Prediction of interresidue contacts with DeepMetaPSICOV in CASP13
Q80752693	Prediction of kinase-specific phosphorylation sites with sequence features by a log-odds ratio approach
Q30379193	Prediction of ligand binding sites using homologous structures and conservation at CASP8.
Q77386247	Prediction of loop geometries using a generalized born model of solvation effects
Q52214249	Prediction of membrane protein types and subcellular locations
Q30351475	Prediction of novel and analogous folds using fragment assembly and fold recognition.
Q51932138	Prediction of peptide structure: how far are we?
Q41955954	Prediction of phenotypes of missense mutations in human proteins from biological assemblies
Q47664031	Prediction of phosphorylation sites based on Krawtchouk image moments
Q28205759	Prediction of possible sites for posttranslational modifications in human gamma crystallins: Effect of glycation on the structure of human gamma‐b‐crystallin as analyzed by molecular modeling
Q51980533	Prediction of protein B-factor profiles
Q45070147	Prediction of protein accessible surface areas by support vector regression
Q54615864	Prediction of protein binding regions.
Q33941503	Prediction of protein cellular attributes using pseudo-amino acid composition
Q57754185	Prediction of protein conformational freedom from distance constraints
Q36584378	Prediction of protein domain boundaries from inverse covariances
Q90900989	Prediction of protein flexibility using a conformationally restrained contact map
Q46213947	Prediction of protein folding class from amino acid composition
Q49265986	Prediction of protein interaction sites from sequence profile and residue neighbor list
Q30367309	Prediction of protein local structures and folding fragments based on building-block library.
Q51911900	Prediction of protein loop geometries in solution
Q30401819	Prediction of protein mutation effects based on dehydration and hydrogen bonding - A large-scale study
Q90058547	Prediction of protein oligomer structures using GALAXY in CASP13
Q30350134	Prediction of protein relative solvent accessibility with a two-stage SVM approach.
Q47236434	Prediction of protein relative solvent accessibility with support vector machines and long-range interaction 3D local descriptor
Q52075238	Prediction of protein secondary structure at 80% accuracy
Q30362848	Prediction of protein secondary structure content for the twilight zone sequences.
Q30352177	Prediction of protein secondary structure content using amino acid composition and evolutionary information.
Q45421787	Prediction of protein secondary structure from circular dichroism using theoretically derived spectra
Q52941135	Prediction of protein secondary structures from conformational biases
Q52070751	Prediction of protein signal sequences and their cleavage sites
Q45967137	Prediction of protein solvent accessibility using support vector machines.
Q46560080	Prediction of protein stability changes for single-site mutations using support vector machines
Q30336225	Prediction of protein structure by emphasizing local side-chain/backbone interactions in ensembles of turn fragments
Q30366952	Prediction of protein structure from ideal forms.
Q47405976	Prediction of protein structure with the coarse-grained UNRES force field assisted by small X-ray scattering data and knowledge-based information
Q30175326	Prediction of protein structure: the problem of fold multiplicity
Q28244166	Prediction of protein subcellular localization
Q52068724	Prediction of protein surface accessibility with information theory.
Q31101728	Prediction of protein tertiary structure using PROFESY, a novel method based on fragment assembly and conformational space annealing
Q34017391	Prediction of protein-glucose binding sites using support vector machines
Q92331123	Prediction of quaternary structure by analysis of hot spot residues in protein-protein interfaces: the case of anthranilate phosphoribosyltransferases
Q38562011	Prediction of secondary structural content of proteins from their amino acid composition alone. I. New analytic vector decomposition methods
Q38562009	Prediction of secondary structural content of proteins from their amino acid composition alone. II. The paradox with secondary structural class
Q30196217	Prediction of secondary structure by evolutionary comparison: application to the alpha subunit of tryptophan synthase
Q33268373	Prediction of side-chain conformations on protein surfaces
Q41882635	Prediction of stability changes upon mutation in an icosahedral capsid
Q47615952	Prediction of strand pairing in antiparallel and parallel beta-sheets using information theory
Q44898281	Prediction of the bonding states of cysteines using the support vector machines based on multiple feature vectors and cysteine state sequences
Q30351051	Prediction of the conformation and geometry of loops in globular proteins: testing ArchDB, a structural classification of loops.
Q39103337	Prediction of the conformation of ice-nucleation protein by conformational energy calculation
Q91945139	Prediction of the initial folding sites and the entire folding processes for Ig-like beta-sandwich proteins
Q30343006	Prediction of the interaction site on the surface of an isolated protein structure by analysis of side chain energy scores.
Q40941083	Prediction of the secondary structure of HIV-1 gp120.
Q73871016	Prediction of the secondary structure of the nicotinic acetylcholine receptor nontransmembrane regions
Q30193331	Prediction of the structure of GroES and its interaction with GroEL.
Q42655710	Prediction of the structure of the replication initiator protein DnaA.
Q40551036	Prediction of the substrate for nonribosomal peptide synthetase (NRPS) adenylation domains by virtual screening
Q30404505	Prediction of the tertiary structure of the alpha-subunit of tryptophan synthase
Q46054195	Prediction of the three-dimensional structure of human growth hormone
Q52244716	Prediction of the three-dimensional structure of proteins using the electrostatic screening model and hierarchic condensation
Q47863720	Prediction of the unknown: inspiring experience with the CAPRI experiment
Q30363102	Prediction of transition metal-binding sites from apo protein structures.
Q30164057	Prediction of transmembrane regions of beta-barrel proteins using ANN- and SVM-based methods.
Q45966232	Prediction of transporter family from protein sequence by support vector machine approach.
Q30370580	Prediction of turn types in protein structure by machine-learning classifiers.
Q57090483	Prediction targets of CASP4
Q36569264	Prediction, refinement, and persistency of transmembrane helix dimers in lipid bilayers using implicit and explicit solvent/lipid representations: microsecond molecular dynamics simulations of ErbB1/B2 and EphA1.
Q45965622	Prediction-based fingerprints of protein-protein interactions.
Q46120384	Predictions of protein flexibility: first-order measures
Q52072059	Predictions of protein segments with the same aminoacid sequence and different secondary structure: a benchmark for predictive methods.
Q28212631	Predictions without templates: New folds, secondary structure, and contacts in CASP5
Q44252315	Predictive crystallization of ribonuclease A via rapid screening of osmotic second virial coefficients
Q45070154	Predictive reconstruction of the mitochondrial iron-sulfur cluster assembly metabolism. II. Role of glutaredoxin Grx5.
Q47307308	Predictive reconstruction of the mitochondrial iron-sulfur cluster assembly metabolism: I. The role of the protein pair ferredoxin-ferredoxin reductase (Yah1-Arh1).
Q47601163	Predisposition of the dark state of rhodopsin to functional changes in structure
Q30403888	Preferred conformational state of the N-terminus section of a bovine growth hormone fragment (residues 96-133) in water is an omega loop
Q102371569	Prefusion spike protein stabilization through computational mutagenesis
Q54635852	Preliminary X-ray analysis of Escherichia coli GMP synthetase: determination of anomalous scattering factors for a cysteinyl mercury derivative.
Q70121400	Preliminary X-ray analysis of crystals of plasminogen activator inhibitor-1
Q65559583	Preliminary X-ray crystallographic analysis ofTritrichomonas foetus inosine-5′-monophosphate dehydrogenase
Q54774139	Preliminary X-ray diffraction analysis of HhaII endonuclease-DNA cocrystals.
Q45785149	Preliminary X-ray diffraction analysis of crystals of tomato aspermy virus (TAV).
Q43444530	Preliminary X-ray diffraction analysis of crystals of turnip yellow mosaic virus (TYMV).
Q41881305	Preliminary X-ray diffraction studies and biochemical characterization of the antitumor protein mitomalcin indicate close similarity to neocarzinostatin
Q44481189	Preliminary crystallographic analysis of an enzyme involved in erythromycin biosynthesis: cytochrome P450eryF.
Q54720639	Preliminary crystallographic analysis of class 3 rat liver aldehyde dehydrogenase.
Q58321559	Preliminary crystallographic characterization of ricin agglutinin
Q72242673	Preparation and characterization of the E168Q site-directed mutant of yeast enolase 1
Q52999918	Preparation and crystallization of a cross-linked complex of bovine adrenodoxin and adrenodoxin reductase
Q57008054	Preparation and initial characterization of crystals of the photoprotein aequorin from Aequorea victoria
Q46800694	Preparation of amino-acid-type selective isotope labeling of protein expressed in Pichia pastoris.
Q51508103	PresCont: predicting protein-protein interfaces utilizing four residue properties.
Q39949452	Present and future challenges and limitations in protein-protein docking
Q30417671	Pressure as a denaturing agent in studies of single-point mutants of an amyloidogenic protein human cystatin c.
Q43676063	Pressure effect on denaturant-induced unfolding of hen egg white lysozyme
Q30351842	Pressure effect on the stability and the conformational dynamics of the D-Galactose/D-Glucose-binding protein from Escherichia coli.
Q30476118	Pressure perturbation calorimetry of apolipoproteins in solution and in model lipoproteins
Q46863955	Pressure perturbation calorimetry of helical peptides
Q27649295	Pressure-induced changes in the solution structure of the GB1 domain of protein G
Q87442896	Pressure-induced conformational switch of an interfacial protein
Q30994627	Pressure-induced structural transition of mature HIV-1 protease from a combined NMR/MD simulation approach
Q67488113	Primary mutations in calmodulin prevent activation of the Ca+ +‐dependent Na+ channel in Paramecium
Q29614750	Primary structure effects on peptide group hydrogen exchange
Q36448475	Primary structure of a precursor to the aspartic proteinase from Rhizomucor miehei shows that the enzyme is synthesized as a zymogen
Q57088249	Primary structure of the common polypeptide chainb from the multi-hemoglobin system of the hydrothermal vent tube wormRiftia pachyptila: An insight on the sulfide binding-site
Q46497685	Primary structure of the reaction center from Rhodopseudomonas sphaeroides
Q30399169	Princeton_TIGRESS 2.0: High refinement consistency and net gains through support vector machines and molecular dynamics in double-blind predictions during the CASP11 experiment
Q30355061	Princeton_TIGRESS: protein geometry refinement using simulations and support vector machines.
Q30559566	Principal component analysis of chemical shift perturbation data of a multiple-ligand-binding system for elucidation of respective binding mechanism.
Q51639725	Principal component and normal mode analysis of proteins; a quantitative comparison using the GroEL subunit
Q57217928	Principal eigenvector of contact matrices and hydrophobicity profiles in proteins
Q27731973	Principles and pitfalls in designing site-directed peptide ligands
Q28217048	Principles of docking: An overview of search algorithms and a guide to scoring functions
Q57808017	Principles of docking: An overview of search algorithms and a guide to scoring functions
Q36952164	Principles of flexible protein-protein docking
Q33281033	Principles of nanostructure design with protein building blocks
Q39855522	Prion protein region 23-32 interacts with tubulin and inhibits microtubule assembly
Q36909356	Prior knowledge or freedom of interpretation? A critical look at a recently published classification of "novel" Zn binding sites
Q92194951	ProDCoNN: Protein design using a convolutional neural network
Q51104952	ProDomAs, protein domain assignment algorithm using center-based clustering and independent dominating set.
Q75209210	ProVal: a protein-scoring function for the selection of native and near-native folds
Q51927404	Probabilistic alignment detects remote homology in a pair of protein sequences without homologous sequence information
Q47430812	Probabilistic description of protein alignments for sequences and structures
Q30329264	Probabilistic sampling of protein conformations: New hope for brute force?
Q80045488	Probe-dependent and nonexponential relaxation kinetics: unreliable signatures of downhill protein folding
Q51050770	Probing a continuum of macro-molecular assembly models with graph templates of complexes
Q31161561	Probing beta-lactamase structure and function using random replacement mutagenesis
Q46794978	Probing electric fields in proteins in solution by NMR spectroscopy
Q46853482	Probing electrostatic interactions and ligand binding in aspartyl-tRNA synthetase through site-directed mutagenesis and computer simulations
Q47430898	Probing flexibility and "induced-fit" phenomena in aldose reductase by comparative crystal structure analysis and molecular dynamics simulations
Q46899112	Probing ligand binding modes of human cytochrome P450 2J2 by homology modeling, molecular dynamics simulation, and flexible molecular docking
Q73393624	Probing local environments of tryptophan residues in proteins: comparison of 19F nuclear magnetic resonance results with the intrinsic fluorescence of soluble human tissue factor
Q51080128	Probing nascent structures in peptides using natural abundance 13C NMR relaxation and reduced spectral density mapping
Q38848944	Probing protease sensitivity of recombinant human erythropoietin reveals α3-α4 inter-helical loop as a stability determinant.
Q48136545	Probing subtle conformational changes induced by phosphorylation and point mutations in the TIR domains of TLR2 and TLR3.
Q40957320	Probing the activation of protein C by the thrombin-thrombomodulin complex using structural analysis, site-directed mutagenesis, and computer modeling
Q30339082	Probing the alpha-complementing domain of E. coli beta-galactosidase with use of an insertional pentapeptide mutagenesis strategy based on Mu in vitro DNA transposition.
Q46905577	Probing the different chaperone activities of the bacterial HSP70-HSP40 system using a thermolabile luciferase substrate
Q77977309	Probing the modelled structure of wheatwin1 by controlled proteolysis and sequence analysis of unfractionated digestion mixtures
Q27765709	Probing the potential glycoprotein binding site of sindbis virus capsid protein with dioxane and model building
Q41895535	Probing the role of interfacial waters in protein–DNA recognition using a hybrid implicit/explicit solvation model
Q27702639	Probing the roles of two tryptophans surrounding the unique zinc coordination site in lipase family I.5
Q38784917	Probing the structural dynamics of the CRISPR-Cas9 RNA-guided DNA-cleavage system by coarse-grained modeling
Q38879619	Probing the structural dynamics of the SNARE recycling machine based on coarse-grained modeling
Q43947460	Probing the structure of the warfarin-binding site on human serum albumin using site-directed mutagenesis
Q73217210	Proceedings of the 3rd meeting on the Critical Assessment of Techniques for Protein Structure Prediction. Asilomar, December 1998
Q83476427	Proceedings of the 4th Meeting on the Critical Assessment of Predicted Interaction (CAPRI), Barcelona, Spain
Q80548333	Proceedings of the Seventh Meeting on the Critical Assessment of Techniques for Protein Structure Prediction. November 26-30, 2006. Pacific Grove, California, USA
Q28145979	Processing and analysis of CASP3 protein structure predictions
Q28218067	Processing and evaluation of predictions in CASP4
Q59443871	Processing and evaluation of predictions in CASP4
Q39606407	Processivity of nucleic acid unwinding and translocation by helicases
Q71671461	Production and crystallization of a selenomethionyl variant of UmuD', an Escherichia coli SOS response protein
Q57209021	Profile-profile methods provide improved fold-recognition: A study of different profile-profile alignment methods
Q48557743	Profiling the array of Ca(v)3.1 variants from the human T-type calcium channel gene CACNA1G: alternative structures, developmental expression, and biophysical variations
Q30350114	Progress and challenges in high-resolution refinement of protein structure models.
Q34698989	Progress from CASP6 to CASP7.
Q46907040	Progress in computation and amide hydrogen exchange for prediction of protein-protein complexes
Q52324562	Progress in fold recognition.
Q52046751	Progress in predicting inter-residue contacts of proteins with neural networks and correlated mutations.
Q28258457	Progress in protein-protein docking: atomic resolution predictions in the CAPRI experiment using RosettaDock with an improved treatment of side-chain flexibility
Q38915827	Progress in super long loop prediction.
Q35627466	Progress in the prediction of pKa values in proteins
Q56979272	Progress in the structural prediction of G protein-coupled receptors: D3 receptor in complex with eticlopride
Q30424386	Progress of 1D protein structure prediction at last
Q30351482	Progress over the first decade of CASP experiments.
Q44125156	Progress toward virtual screening for drug side effects.
Q30164198	Progressive combinatorial algorithm for multiple structural alignments: application to distantly related proteins
Q45012035	Projection of Monte Carlo and molecular dynamics trajectories onto the normal mode axes: human lysozyme
Q41914753	Proline in alpha-helix: stability and conformation studied by dynamics simulation
Q43629656	Proline-induced hinges in transmembrane helices: possible roles in ion channel gating
Q30157751	Prolylproline unit in model peptides and in fragments from databases
Q51791742	Propensity vectors of low-ASA residue pairs in the distinction of protein interactions
Q68704281	Properties of a second sensory receptor protein in Halobacterium halobium phototaxis
Q45276526	Properties of integral membrane protein structures: derivation of an implicit membrane potential.
Q45229454	Properties of polyproline II, a secondary structure element implicated in protein-protein interactions
Q80045491	Property-based sequence representations do not adequately encode local protein folding information
Q27641380	Proposed amino acid sequence and the 1.63 A X-ray crystal structure of a plant cysteine protease, ervatamin B: some insights into the structural basis of its stability and substrate specificity
Q28293819	Proposed structural models of the prothrombinase (FXa-FVa) complex
Q46546900	Protease pro region required for folding is a potent inhibitor of the mature enzyme.
Q68236082	Proteases of enhanced stability: characterization of a thermostable variant of subtilisin
Q90747077	Protein adaptation to high hydrostatic pressure: Computational analysis of the structural proteome
Q81258728	Protein classification based on text document classification techniques
Q31139777	Protein classification with imbalanced data
Q46068059	Protein conformational landscapes: energy minimization and clustering of a long molecular dynamics trajectory
Q45996366	Protein conformational transitions coupled to binding in molecular recognition of unstructured proteins: deciphering the effect of intermolecular interactions on computational structure prediction of the p27Kip1 protein bound to the cyclin A-cyclin-
Q51911720	Protein conformational transitions explored by mixed elastic network models
Q42621326	Protein conformer selection by sequence-dependent packing contacts in crystals of 3-phosphoglycerate kinase
Q45944818	Protein contact prediction by integrating deep multiple sequence alignments, coevolution and machine learning.
Q44998310	Protein contact prediction using patterns of correlation
Q40741195	Protein crystallography for all.
Q53042799	Protein cutoff scanning: A comparative analysis of cutoff dependent and cutoff free methods for prospecting contacts in proteins.
Q34436089	Protein design on computers. Five new proteins: Shpilka, Grendel, Fingerclasp, Leather, and Aida
Q46827672	Protein design simulations suggest that side-chain conformational entropy is not a strong determinant of amino acid environmental preferences
Q52062727	Protein docking using a genetic algorithm
Q51151900	Protein docking using case-based reasoning
Q52080524	Protein docking using spherical polar Fourier correlations
Q45965397	Protein docking using surface matching and supervised machine learning.
Q80538483	Protein domain annotation with integration of heterogeneous information sources
Q30399247	Protein domain assignment from the recurrence of locally similar structures
Q52033388	Protein domain identification and improved sequence similarity searching using PSI-BLAST.
Q52256509	Protein domain movements: detection of rigid domains and visualization of hinges in comparisons of atomic coordinates
Q45249247	Protein domain of unknown function DUF1023 is an alpha/beta hydrolase
Q62654659	Protein dynamics analysis reveals that missense mutations in cancer-related genes appear frequently on hinge-neighboring residues
Q79416234	Protein dynamics from X-ray crystallography: anisotropic, global motion in diffuse scattering patterns
Q44932771	Protein electrostatics and pKa blind predictions; contribution from empirical predictions of internal ionizable residues.
Q38666970	Protein features as determinants of wild-type glycoside hydrolase thermostability
Q34440277	Protein flexibility and rigidity predicted from sequence
Q84685413	Protein flexibility from discrete molecular dynamics simulations using quasi-physical potentials
Q43629667	Protein flexibility predictions using graph theory
Q43648923	Protein fluorescence quenching by small molecules: protein penetration versus solvent exposure
Q41649019	Protein fold analysis of the B30.2-like domain
Q71961398	Protein fold recognition and dynamics in the space of contact maps
Q52077268	Protein fold recognition by total alignment probability
Q57746713	Protein fold recognition score functions: Unusual construction strategies
Q27861091	Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons
Q30165171	Protein folding in mode space: a collective coordinate approach to structure prediction
Q41690266	Protein folding in the landscape perspective: Chevron plots and non-arrhenius kinetics
Q30400486	Protein folding kinetics by combined use of rapid mixing techniques and NMR observation of individual amide protons
Q52237311	Protein folding mechanisms and the multidimensional folding funnel
Q51647609	Protein folding simulation with genetic algorithm and supersecondary structure constraints
Q57135272	Protein folding simulation with solvent-induced force field: folding pathway ensemble of three-helix-bundle proteins
Q30329263	Protein folding: Looping from hydrophobic nuclei
Q41034558	Protein folding: predicting predicting
Q74252605	Protein folds from pair interactions: A blind test in fold recognition
Q78955240	Protein fragment clustering and canonical local shapes
Q42414721	Protein function annotation by local binding site surface similarity
Q53679864	Protein heat capacity reflects the dynamics of enthalpy exchange between the single macromolecule and the surroundings
Q30363180	Protein homology detection and fold inference through multiple alignment entropy profiles.
Q84801600	Protein homomers in point‐group assembly: Symmetry making and breaking are specific and distinctive in their codes of chemical alphabet in side chains
Q68697925	Protein hydrophobicity: is it the sum of its parts?
Q46794973	Protein kinase C isozymes and their selectivity towards ruboxistaurin
Q46129960	Protein kinase resource: an integrated environment for phosphorylation research
Q78955236	Protein local structure prediction from sequence
Q34097299	Protein loop closure using orientational restraints from NMR data
Q34292837	Protein loop modeling by using fragment assembly and analytical loop closure
Q51568651	Protein loop selection using orientation-dependent force fields derived by parameter optimization
Q30351615	Protein loop structure prediction with flexible stem geometries.
Q99401364	Protein loops with multiple meta-stable conformations: a challenge for sampling and scoring methods
Q38091029	Protein misfolding in the late-onset neurodegenerative diseases: common themes and the unique case of amyotrophic lateral sclerosis.
Q90919878	Protein model discrimination attempts using mutational sensitivity, predicted secondary structure, and model quality information
Q33305650	Protein model quality assessment prediction by combining fragment comparisons and a consensus C(alpha) contact potential
Q52281057	Protein modeling by multiple sequence threading and distance geometry.
Q35450334	Protein models docking benchmark 2.
Q37129861	Protein models: the Grand Challenge of protein docking
Q57134681	Protein molecular dynamics with electrostatic force entirely determined by a single Poisson-Boltzmann calculation
Q57077682	Protein molecular dynamics with the generalized born/ACE solvent model
Q43030167	Protein rigidity and thermophilic adaptation
Q37937535	Protein secondary structure and circular dichroism: a practical guide
Q47715236	Protein secondary structure assignment through Voronoï tessellation
Q81547710	Protein secondary structure prediction with dihedral angles
Q74054779	Protein sequence threading: Averaging over structures
Q35947259	Protein side chain conformation predictions with an MMGBSA energy function
Q30360147	Protein side-chain modeling with a protein-dependent optimized rotamer library.
Q44252308	Protein side-chain rearrangement in regions of point mutations
Q30339081	Protein simple sequence conservation.
Q28236405	Protein simulations using techniques suitable for very large systems: the cell multipole method for nonbond interactions and the Newton-Euler inverse mass operator method for internal coordinate dynamics
Q28818852	Protein social behavior makes a stronger signal for partner identification than surface geometry
Q68566676	Protein stability and electrostatic interactions between solvent exposed charged side chains
Q30407525	Protein stability and in vivo concentration of missense mutations in phenylalanine hydroxylase.
Q72416539	Protein stability parameters measured by hydrogen exchange
Q50517955	Protein strain in blue copper proteins studied by free energy perturbations
Q73379973	Protein structural alignments and functional genomics
Q57065004	Protein structural domains: Analysis of the 3Dee domains database
Q57065016	Protein structural domains: Analysis of the 3Dee domains database
Q30326372	Protein structure alignment using a genetic algorithm.
Q30425192	Protein structure and the sequential structure of mRNA: alpha-helix and beta-sheet signals at the nucleotide level
Q30327109	Protein structure comparison using the markov transition model of evolution.
Q30380138	Protein structure determination by conformational space annealing using NMR geometric restraints.
Q30365837	Protein structure mining using a structural alphabet.
Q47916176	Protein structure model refinement in CASP12 using short and long molecular dynamics simulations in implicit solvent
Q47380009	Protein structure modeling and refinement by global optimization in CASP12.
Q30353045	Protein structure modeling for CASP10 by multiple layers of global optimization.
Q30319684	Protein structure modeling indicates hexahistidine-tag interference with enzyme activity
Q90653346	Protein structure prediction assisted with sparse NMR data in CASP13
Q30383511	Protein structure prediction begins well but ends badly.
Q30424389	Protein structure prediction by threading methods: evaluation of current techniques
Q30380286	Protein structure prediction center in CASP8.
Q30426891	Protein structure prediction force fields: parametrization with quasi-newtonian dynamics
Q30351472	Protein structure prediction in CASP6 using CHIMERA and FAMS.
Q79209995	Protein structure prediction of CASP5 comparative modeling and fold recognition targets using consensus alignment approach and 3D assessment
Q47756295	Protein structure prediction using Rosetta in CASP12.
Q30329570	Protein structure prediction using a combination of sequence-based alignment, constrained energy minimization, and structural alignment.
Q30401241	Protein structure prediction using a docking-based hierarchical folding scheme
Q30351470	Protein structure prediction using a variety of profile libraries and 3D verification.
Q90646320	Protein structure prediction using multiple deep neural networks in the 13th Critical Assessment of Protein Structure Prediction (CASP13)
Q30378826	Protein structure prediction using residue- and fragment-environment potentials in CASP11.
Q91778709	Protein structure prediction using sparse NOE and RDC restraints with Rosetta in CASP13
Q38629307	Protein structure prediction: making AWSEM AWSEM-ER by adding evolutionary restraints
Q30375937	Protein structure refinement by optimization.
Q30377414	Protein structure refinement via molecular-dynamics simulations: What works and what does not?
Q30379991	Protein structure refinement with adaptively restrained homologous replicas.
Q93092064	Protein tertiary structure modeling driven by deep learning and contact distance prediction in CASP13
Q52220825	Protein tertiary structure prediction using a branch and bound algorithm
Q30367570	Protein thermal stabilization by charged compatible solutes: Computational studies in rubredoxin from Desulfovibrio gigas.
Q52077270	Protein threading using PROSPECT: design and evaluation
Q30356324	Protein under pressure: molecular dynamics simulation of the arc repressor.
Q51639175	Protein unfolding at interfaces: slow dynamics of alpha-helix to beta-sheet transition
Q28258488	Protein-Protein Docking Benchmark 2.0: an update
Q79522519	Protein-RNA contacts at crystal packing surfaces
Q79448967	Protein-RNA interactions: structural analysis and functional classes
Q44242205	Protein-based virtual screening of chemical databases. II. Are homology models of G-Protein Coupled Receptors suitable targets?
Q30380928	Protein-binding site prediction based on three-dimensional protein modeling.
Q68763748	Protein-drug interactions: characterization of inhibitor binding in complexes of DHFR with trimethoprim and related derivatives
Q43558037	Protein-flavonol interaction: fluorescence spectroscopic study
Q30383790	Protein-fold recognition using an improved single-source K diverse shortest paths algorithm.
Q51626047	Protein-inhibitor flexible docking by a multicanonical sampling: native complex structure with the lowest free energy and a free-energy barrier distinguishing the native complex from the others
Q36544700	Protein-ligand docking: current status and future challenges
Q46668372	Protein-nucleic acid recognition: statistical analysis of atomic interactions and influence of DNA structure
Q39245081	Protein-protein and peptide-protein docking and refinement using ATTRACT in CAPRI.
Q50882321	Protein-protein association rates captured in a single geometric parameter
Q57976304	Protein-protein binding is often associated with changes in protonation state
Q41891375	Protein-protein docking benchmark version 3.0.
Q51897092	Protein-protein docking by simulating the process of association subject to biochemical constraints
Q50919250	Protein-protein docking in CAPRI using ATTRACT to account for global and local flexibility
Q57814824	Protein-protein docking of electron transfer complexes: Cytochromecoxidase and cytochromec
Q28208464	Protein-protein docking predictions for the CAPRI experiment
Q33217994	Protein-protein docking using 3D-Dock in rounds 3, 4, and 5 of CAPRI.
Q51665410	Protein-protein docking with binding site patch prediction and network-based terms enhanced combinatorial scoring.
Q51906617	Protein-protein docking: progress in CAPRI rounds 6-12 using a combination of methods: the introduction of steered solvated molecular dynamics
Q71374340	Protein-protein interaction at crystal contacts
Q38498009	Protein-protein interaction network-based detection of functionally similar proteins within species
Q45935765	Protein-protein interactions at an enzyme-substrate interface: characterization of transient reaction intermediates throughout a full catalytic cycle of Escherichia coli thioredoxin reductase.
Q83216415	Protein-protein interactions in actin-myosin binding and structural effects of R405Q mutation: a molecular dynamics study
Q63979795	Protein-protein interactions: Analysis of a false positive GST pulldown result
Q47619897	Protein-protein interfaces: analysis of amino acid conservation in homodimers
Q52465000	Protein-protein recognition analyzed by docking simulation
Q51924434	Protein-protein recognition and interaction hot spots in an antigen-antibody complex: free energy decomposition identifies "efficient amino acids".
Q52224060	Protein-protein recognition: exploring the energy funnels near the binding sites
Q30388852	Protein-protein structure prediction by scoring molecular dynamics trajectories of putative poses.
Q34437618	Protein-spanning water networks and implications for prediction of protein-protein interactions mediated through hydrophobic effects
Q80559801	Protein-thiol substitution or protein dethiolation by thiol/disulfide exchange reactions: the albumin model
Q47596418	Protein-water interactions in ribonuclease A and angiogenin: a molecular dynamics study
Q38188308	Proteins and peptides in water-restricted environments
Q47603412	Proteins of the same fold and unrelated sequences have similar amino acid composition
Q42093255	Protein–protein docking benchmark version 4.0
Q57814814	Protein–protein docking of electron transfer complexes: Cytochrome c oxidase and cytochrome c
Q80448968	Proteochemometric analysis of small cyclic peptides' interaction with wild-type and chimeric melanocortin receptors
Q51920356	Proteochemometric modeling reveals the interaction site for Trp9 modified alpha-MSH peptides in melanocortin receptors
Q74419065	Proteolysis as a probe of thermal unfolding of cytochrome C
Q70388086	Proteolytic dissection of a hapten binding site
Q52003359	Proteomic signatures: amino acid and oligopeptide compositions differentiate among phyla
Q47622317	ProtoMap: automatic classification of protein sequences, a hierarchy of protein families, and local maps of the protein space
Q43676091	Protochlorophyllide oxidoreductase: a homology model examined by site-directed mutagenesis
Q51918183	Proton pathways and H+/Cl- stoichiometry in bacterial chloride transporters
Q81230775	Proton pathways in a [NiFe]-hydrogenase: A theoretical study
Q90612993	Proton relay network in P450cam formed upon docking of putidaredoxin
Q46655444	Proton transfer in a Thr200His mutant of human carbonic anhydrase II.
Q41815761	Protonate3D: assignment of ionization states and hydrogen coordinates to macromolecular structures
Q80595829	Protonation state and substrate binding to B2 metallo-beta-lactamase CphA from Aeromonas hydrofila
Q90564487	Protonation state of the selectivity filter of bacterial voltage-gated sodium channels is modulated by ions
Q40696079	Protonation states of active-site lysines of penicillin-binding protein 6 from Escherichia coli and the mechanistic implications.
Q54434623	Protonless 13C direct detection NMR: characterization of the 37 kDa trimeric protein CutA1.
Q42253991	Prots: A fragment based protein thermo‐stability potential
Q33460006	PseqIP: a nonredundant and exhaustive protein sequence data bank generated from 4 major existing collections
Q52256499	Pseudocontact shifts as constraints for energy minimization and molecular dynamics calculations on solution structures of paramagnetic metalloproteins
Q80168581	Pump-probe molecular dynamics as a tool for studying protein motion and long range coupling
Q73428010	Purification and crystallization of Pseudomonas aeruginosa chloramphenicol acetyltransferase
Q41170735	Purification and crystallization of a complex between human interferon gamma receptor (extracellular domain) and human interferon gamma
Q54613001	Purification and crystallization of a schistosomal glutathione S-transferase.
Q52441418	Purification and crystallization of insecticidal delta-endotoxin CryIIIB2 from Bacillus thuringiensis
Q44260172	Purification and preliminary crystallographic studies on the sporulation response regulatory phosphotransferase protein, Spo0B, from Bacillus subtilis
Q104111707	Purification, characterization and crystal structure of YhdA-type azoreductase from Bacillus velezensis
Q70980749	Purification, characterization, crystallization, and preliminary X-ray results from Paracoccus denitrificans porin
Q71374372	Purification, crystallization, and preliminary X-ray analysis of Bacillus subtilis ferrochelatase
Q54602213	Purification, crystallization, and preliminary X-ray analysis of PepX, an X-prolyl dipeptidyl aminopeptidase from Lactococcus lactis.
Q50144420	Purification, crystallization, and preliminary X-ray diffraction analyses of the bacterial chemotaxis receptor modifying enzymes.
Q38298248	Purification, crystallization, and preliminary X-ray diffraction analysis of even-skipped homeodomain complexed to DNA.
Q45990770	Purification, crystallization, and preliminary X-ray studies of 10-formyltetrahydrofolate synthetase from Clostridia acidici-urici.
Q38322022	Purification, crystallization, and preliminary X-ray studies on the rhizome lectin from stinging nettle and its complex with NN'N"-triacetylchitotriose
Q30468986	Purification, crystallization, and preliminary crystallographic analysis of 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase from Escherichia coli
Q71660312	Purification, crystallization, and preliminary x-ray diffraction studies of tRNA-guanine transglycosylase from Zymomonas mobilis
Q36849665	Purification, crystallization, and preliminary x-ray studies of a bifunctional 5,10-methenyl/methylene-tetrahydrofolate cyclohydrolase/dehydrogenase from Escherichia coli
Q54589429	Purification, stabilization, and crystallization of a modular protein: Grb2.
Q45029743	Purine salvage in Methanocaldococcus jannaschii: Elucidating the role of a conserved cysteine in adenine deaminase
Q44607630	Putative cholesterol-binding sites in human immunodeficiency virus (HIV) coreceptors CXCR4 and CCR5.
Q92445268	Putative structural rearrangements associated with the interaction of macrocyclic inhibitors with norovirus 3CL protease
Q34316219	Pyrrolidone carboxyl peptidase (Pcp): an enzyme that removes pyroglutamic acid (pGlu) from pGlu-peptides and pGlu-proteins
Q30353222	QBES: predicting real values of solvent accessibility from sequences by efficient, constrained energy optimization.
Q42739061	QM/MM linear response method distinguishes ligand affinities for closely related metalloproteins
Q46500571	QM/MM modeling the Ras-GAP catalyzed hydrolysis of guanosine triphosphate.
Q51134217	QM/MM studies on the calcium-assisted β-elimination mechanism of pectate lyase from bacillus subtilis
Q43818080	QM/MM study of the C-C coupling reaction mechanism of CYP121, an essential cytochrome p450 of Mycobacterium tuberculosis.
Q30365138	QMEAN: A comprehensive scoring function for model quality assessment.
Q30665587	QSAR: hydropathic analysis of inhibitors of the p53-mdm2 interaction
Q33888045	QSD quadratic shape descriptors. 2. Molecular docking using quadratic shape descriptors (QSDock).
Q30350531	Quantifying allosteric effects in proteins.
Q71671449	Quantifying biological specificity: the statistical mechanics of molecular recognition
Q47296179	Quantifying the effect of burial of amino acid residues on protein stability
Q51784692	Quantifying the evolutionary divergence of protein structures: the role of function change and function conservation.
Q34664245	Quantifying the relationship of protein burying depth and sequence
Q47771215	Quantitative analysis and prediction of curvature in leucine-rich repeat proteins
Q52070052	Quantitative comparison of the ability of hydropathy scales to recognize surface beta-strands in proteins
Q41489269	Quantitative delineation of how breathing motions open ligand migration channels in myoglobin and its mutants
Q30367568	Quantitative expression of protein heterogeneity: Response of amino acid side chains to their local environment.
Q47174762	Quantitative modeling of peptide binding to TAP using support vector machine
Q68878435	Quantitative organization of the known protein x-ray structures. I. Methods and short-length-scale results
Q46251096	Quantitative structure activity relationship of IA3-like peptides as aspartic proteinase inhibitors
Q55120704	Quantitative use of chemical shifts for the modeling of protein complexes
Q46661986	Quantum computational analysis for drug resistance of HIV-1 reverse transcriptase to nevirapine through point mutations
Q80389895	Quantum descriptors for biological macromolecules from linear-scaling electronic structure methods
Q38939533	Quantum mechanical electronic structure calculation reveals orientation dependence of hydrogen bond energy in proteins
Q54623263	Quantum mechanical model assembly study on the energetics of binding of arabinose, fucose, and galactose to L-arabinose-binding protein.
Q30328502	Quantum mechanics simulation of protein dynamics on long timescale.
Q46403165	Quantum study of mutational effect in binding of efavirenz to HIV-1 RT.
Q84789809	Quasi-harmonic fluctuations of two bound peptides
Q46159941	Quaternary structure effects on the hexacoordination equilibrium in rice hemoglobin rHb1: insights from molecular dynamics simulations
Q45554919	Quaternary structure is critical for protein display on capsid-like particles (CLPs): efficient generation of hepatitis B virus CLPs presenting monomeric but not dimeric and tetrameric fluorescent proteins.
Q99633251	Quaternary variations in the structural assembly of N-acetylglucosamine-6-phosphate deacetylase from Pasteurella multocida
Q30402478	Quaternion-based definition of protein secondary structure straightness and its relationship to Ramachandran angles
Q50797771	R248Q mutation--Beyond p53-DNA binding.
Q50660564	RBRDetector: improved prediction of binding residues on RNA-binding protein structures using complementary feature- and template-based strategies
Q41110819	RBRIdent: An algorithm for improved identification of RNA-binding residues in proteins from primary sequences
Q53536105	RCC1-like repeat proteins: a pangenomic, structurally diverse new superfamily of beta-propeller domains
Q79210081	RDOCK: Refinement of rigid‐body protein docking predictions
Q29614749	RECOORD: a recalculated coordinate database of 500+ proteins from the PDB using restraints from the BioMagResBank
Q30375449	REMO: A new protocol to refine full atomic protein models from C-alpha traces by optimizing hydrogen-bonding networks
Q46937892	RIP death domain structural interactions implicated in TNF-mediated proliferation and survival
Q30323115	RMS/coverage graphs: a qualitative method for comparing three-dimensional protein structure predictions.
Q90771209	RMSD analysis of structures of the bacterial protein FimH identifies five conformations of its lectin domain
Q30552721	RNA polymerase II flexibility during translocation from normal mode analysis
Q51933455	ROSETTALIGAND: protein-small molecule docking with full side-chain flexibility
Q57902423	Rab7: NMR and kinetics analysis of intact and C-terminal truncated constructs
Q73134811	Rab7: crystallization of intact and C-terminal truncated constructs complexed with GDP and GppNHp
Q88512044	Radiation chemists look at damage in redox proteins induced by X-rays
Q90984014	Ramachandran maps for side chains in globular proteins
Q129830448	Random, de novo, and conserved proteins: How structure and disorder predictors perform differently
Q51149982	Rank information: a structure-independent measure of evolutionary trace quality that improves identification of protein functional sites
Q41666440	Ranking ligand binding affinities with avidin: a molecular dynamics-based interaction energy study
Q51050723	Ranking multiple docking solutions based on the conservation of inter‐residue contacts
Q30365830	Ranking predicted protein structures with support vector regression.
Q60761692	Ranking the factors that contribute to protein β-sheet folding
Q90297006	Rapid and accurate structure-based therapeutic peptide design using GPU accelerated thermodynamic integration
Q51975402	Rapid assessment of contact-dependent secondary structure propensity: relevance to amyloidogenic sequences
Q52074687	Rapid automatic detection and alignment of repeats in protein sequences
Q31119238	Rapid calculation of the solution scattering profile from a macromolecule of known structure
Q36952014	Rapid comparison of properties on protein surface
Q44784463	Rapid protein-ligand docking using soft modes from molecular dynamics simulations to account for protein deformability: binding of FK506 to FKBP.
Q24633589	Raptorx: Exploiting structure information for protein alignment by statistical inference
Q54737044	Ras interaction with the GTPase-activating protein (GAP).
Q42159713	Rate of beta-structure formation in polypeptides
Q47972577	Ratio of ellipticities between 192 and 208 nm (R1 ): An effective electronic circular dichroism parameter for characterization of the helical components of proteins and peptides.
Q30157141	Rational design of amyloid beta peptide-binding proteins: pseudo-Abeta beta-sheet surface presented in green fluorescent protein binds tightly and preferentially to structured Abeta
Q27649614	Rational design of peptides active against the gram positive bacteria Staphylococcus aureus
Q45159356	Rational discovery of a novel interface for a coactivator in the peroxisome proliferator-activated receptor gamma: theoretical implications of impairment in type 2 diabetes mellitus
Q34669702	Rational genomics I: antisense open reading frames and codon bias in short-chain oxido reductase enzymes and the evolution of the genetic code
Q44667171	Rational proteomics I. Fingerprint identification and cofactor specificity in the short-chain oxidoreductase (SCOR) enzyme family.
Q41891997	Rational proteomics II: electrostatic nature of cofactor preference in the short-chain oxidoreductase (SCOR) enzyme family
Q27665808	Re-engineering specificity in 1,3-1, 4-β-glucanase to accept branched xyloglucan substrates
Q44496092	Re: Watts et al. Proteins 2002;48:161-168.
Q44496103	Reaction mechanism of caspases: insights from QM/MM Car-Parrinello simulations.
Q42681280	Reaction path and free energy calculations of the transition between alternate conformations of HIV-1 protease
Q39673538	Reactivation of mutant p53: Constraints on mechanism highlighted by principal component analysis of the DNA binding domain
Q27765265	Reactivation of the totally inactive pancreatic lipase RP1 by structure-predicted point mutations
Q58882356	Reading the three-dimensional structure of lattice model-designed proteins from their amino acid sequence
Q52022851	Real value prediction of solvent accessibility from amino acid sequence
Q51966304	Real value prediction of solvent accessibility in proteins using multiple sequence alignment and secondary structure.
Q51918600	Real-SPINE: an integrated system of neural networks for real-value prediction of protein structural properties
Q34436712	Real-time ligand binding pocket database search using local surface descriptors
Q30367302	Real-value prediction of backbone torsion angles.
Q39263823	Rebuilding a macromolecular membrane complex at the atomic scale: case of the Kir6.2 potassium channel coupled to the muscarinic acetylcholine receptor M2.
Q47643233	Rebuilding flavodoxin from C alpha coordinates: a test study
Q44165209	Rebuilt 3D structure of the chloroplast f1 ATPase-tentoxin complex.
Q70500337	Recent Developments in Deep Learning Applied to Protein Structure Prediction
Q45172695	Receptor rigidity and ligand mobility in trypsin-ligand complexes
Q27621689	Receptor-binding conformation of the "ELR" motif of IL-8: X-ray structure of the L5C/H33C variant at 2.35 A resolution
Q62153412	Receptor-specific scoring functions derived from quantum chemical models improve affinity estimates for in-silico drug discovery
Q52072064	Receptors coupling to G proteins: is there a signal behind the sequence?
Q44542011	Reciprocal control of retinal rod cyclic GMP phosphodiesterase by its gamma subunit and transducin
Q73594366	Recognition and architecture of the framework structure of protein
Q74464021	Recognition and interaction of small rings with the ricin A-chain binding site
Q54341270	Recognition between a short unstructured peptide and a partially folded fragment leads to the thioredoxin fold sharing native-like dynamics
Q79992401	Recognition of Cdk2 by Cdk7
Q38774504	Recognition of HIV-inactivating peptide triazoles by the recombinant soluble Env trimer, BG505 SOSIP.664.
Q98295347	Recognition of LD motifs by the Focal Adhesion Targeting Domains of FAK and PYK2: Insights from Molecular Dynamics Simulations
Q41675248	Recognition of a protein fold in the context of the Structural Classification of Proteins (SCOP) classification
Q47715209	Recognition of coarse-grained protein tertiary structure
Q72200793	Recognition of distantly related proteins through energy calculations
Q28249658	Recognition of errors in three-dimensional structures of proteins
Q47625148	Recognition of native structure from complete enumeration of low-resolution models with constraints
Q27765264	Recognition of single-stranded DNA by nuclease P1: High resolution crystal structures of complexes with substrate analogs
Q34676752	Recognition of β-calcineurin by the domains of calmodulin: thermodynamic and structural evidence for distinct roles
Q51975052	Recognizing protein folds by cluster distance geometry
Q52210953	Recognizing very distant sequence relationships among proteins by family profile analysis
Q45930668	Recombinant HIV1 protease secreted by Saccharomyces cerevisiae correctly processes myristylated gag polyprotein.
Q45156863	Recombinant antineuraminidase single chain antibody: expression, characterization, and crystallization in complex with antigen.
Q46941745	Reconciling the "old" and "new" views of protein allostery: a molecular simulation study of chemotaxis Y protein (CheY).
Q30757788	Recovering the true targets of specific ligands by virtual screening of the protein data bank
Q52047756	Recurrence quantification analysis reveals interaction partners in paramyxoviridae envelope glycoproteins
Q30195432	Recurrent alpha beta loop structures in TIM barrel motifs show a distinct pattern of conserved structural features.
Q52076418	Recurrent oligomers in proteins: an optimal scheme reconciling accurate and concise backbone representations in automated folding and design studies
Q30995758	Redesigning the DNA-binding specificity of a zinc finger protein: a data base-guided approach
Q40780634	Redesigning the hydrophobic core of a model beta-sheet protein: destabilizing traps through a threading approach
Q38931111	Redesigning the stereospecificity of tyrosyl-tRNA synthetase
Q50452689	Redesigning the type II' β-turn in green fluorescent protein to type I': implications for folding kinetics and stability.
Q34634076	Redox properties and evolution of human glutaredoxins
Q30371317	Reduced alphabet for protein folding prediction.
Q46969641	Reducing CDK4/6-p16(INK4a) interface. Computational alanine scanning of a peptide bound to CDK6 protein.
Q27618179	Refined crystal structure (2.3 A) of a double-headed winged bean alpha-chymotrypsin inhibitor and location of its second reactive site
Q27734159	Refined crystal structure and mutagenesis of human granulocyte-macrophage colony-stimulating factor
Q27619399	Refined solution structure of the C-terminal DNA-binding domain of human immunovirus-1 integrase
Q30427772	Refined solution structure of the anti-mammal and anti-insect LqqIII scorpion toxin: Comparison with other scorpion toxins
Q90179671	Refined structure of BeM9 reveals arginine hand, an overlooked structural motif in scorpion toxins affecting sodium channels
Q70726283	Refined structure of bovine carbonic anhydrase III at 2.0 A resolution
Q27728532	Refined structure of human carbonic anhydrase II at 2.0 A resolution
Q43776861	Refined structure of melittin bound to perdeuterated dodecylphosphocholine micelles as studied by 2D-NMR and distance geometry calculation
Q27733724	Refined structures of bobwhite quail lysozyme uncomplexed and complexed with the HyHEL-5 Fab fragment
Q35848801	Refinement by shifting secondary structure elements improves sequence alignments
Q40925024	Refinement of 3D models of horseradish peroxidase isoenzyme C: predictions of 2D NMR assignments and substrate binding sites
Q42615724	Refinement of NMR-determined protein structures with database derived mean-force potentials
Q30979462	Refinement of X-ray data on dual cosubstrate specificity of CK2 kinase by free energy calculations based on molecular dynamics simulation
Q43194436	Refinement of noncalorimetric determination of the change in heat capacity, DeltaC(p), of protein unfolding and validation across a wide temperature range
Q98165873	Refinement of pairwise potentials via logistic regression to score protein-protein interactions
Q30415550	Refinement of protein structure homology models via long, all-atom molecular dynamics simulations
Q27860639	Refinement of protein structures in explicit solvent
Q47580210	Refinement of protein termini in template-based modeling using conformational space annealing
Q58106950	Refinement of protein-protein complexes in contact map space with metadynamics simulations
Q27664884	Refinement of the NMR structures for acyl carrier protein with scalar coupling data
Q57013562	Refinement of unbound protein docking studies using biological knowledge
Q30415183	Refinement of unreliable local regions in template-based protein models
Q42582708	Refining homology models by combining replica-exchange molecular dynamics and statistical potentials
Q30374452	Refining near-native protein-protein docking decoys by local resampling and energy minimization
Q40656802	Refining structural and functional predictions for secretasome components by comparative sequence analysis
Q40359573	Refining the treatment of membrane proteins by coarse-grained models
Q36885864	Refolding simulations of an isolated fragment of barnase into a native-like β hairpin: Evidence for compactness and hydrogen bonding as concurrent stabilizing factors
Q46668125	Region-specific role of water in collagen unwinding and assembly
Q30380933	Regional covariation and its application for predicting protein contact patches.
Q44379439	Registering alpha-helices and beta-strands using backbone C-H...O interactions
Q35531137	Regulation of oxygen affinity by quaternary enhancement: does hemoglobin Ypsilanti represent an allosteric intermediate?
Q44109422	Regulatory mechanism of the light-activable allosteric switch LOV-TAP for the control of DNA binding: a computer simulation study.
Q84597811	Relation between flexibility and positively selected HIV-1 protease mutants against inhibitors
Q45804029	Relation between pH, structure, and absorption spectrum of Cerulean: a study by molecular dynamics and TD DFT calculations.
Q47406551	Relationship between chaperone activity and oligomeric size of recombinant human alphaA- and alphaB-crystallin: a tryptic digestion study
Q57753048	Relationship between energy distribution and fold stability: Insights from molecular dynamics simulations of native and mutant proteins
Q62898923	Relationship between enzyme activity and dimeric structure of recombinant HIV-1 reverse transcriptase
Q45143295	Relationship between local structural entropy and protein thermostability
Q30343973	Relationship between multiple sequence alignments and quality of protein comparative models.
Q30333351	Relationship between protein structures and disulfide-bonding patterns.
Q44898278	Relationships between amino acid sequence and backbone torsion angle preferences.
Q43026125	Relationships between functional subclasses and information contained in active-site and ligand-binding residues in diverse superfamilies
Q30430531	Relationships between protein sequence and structure patterns based on residue contacts
Q57133963	Relative free energy of binding and binding mode calculations of HIV-1 RT inhibitors based on dock-MM-PB/GS
Q44566278	Relative stability of protein structures determined by X-ray crystallography or NMR spectroscopy: a molecular dynamics simulation study
Q33263222	Relative tolerance of mesostable and thermostable protein homologs to extensive mutation
Q33380655	Relaxation data in NMR structure determination: model calculations for the lysozyme-Gd3+ complex
Q30399241	Remeasuring HEWL pK(a) values by NMR spectroscopy: methods, analysis, accuracy, and implications for theoretical pK(a) calculations
Q48882047	Remembering Cy Levinthal
Q80594695	Remote homolog detection using local sequence-structure correlations
Q51898573	Remote homology detection of integral membrane proteins using conserved sequence features
Q42621333	Reorganization in apo- and holo-beta-lactoglobulin upon protonation of Glu89: molecular dynamics and pKa calculations
Q31086772	Repacking of hydrophobic residues in a stable mutant of apocytochrome b562 selected by phage-display and proteolysis
Q46264300	Repair of impurity-poisoned protein crystal surfaces
Q43565759	Replacement of thrombin residue G184 with Lys or Arg fails to mimic Na+ binding
Q51670405	ReplicOpter: a replicate optimizer for flexible docking.
Q46552313	Replica exchange molecular dynamics simulation of cross-fibrillation of IAPP and PrP106-126.
Q73870991	Report on the 1997 Johns Hopkins protein folding meeting
Q30409446	Representing and comparing protein folds and fold families using three-dimensional shape-density representations.
Q36828221	Requirements for perpendicular helix pairing
Q48215772	Rescore protein-protein docked ensembles with an interface contact statistics.
Q31122954	Residual structure in disordered peptides and unfolded proteins from multivariate analysis and ab initio simulation of Raman optical activity data
Q97591127	Residue Interaction Dynamics in Vaucheria Aureochrome1 LOV: Bridging Theory and Experiments
Q81489833	Residue conservation in viral capsid assembly
Q52066467	Residue frequencies and pairing preferences at protein-protein interfaces
Q48228790	Residue packing in globular and intrinsically disordered proteins
Q90299990	Residue-level determinants of angiopoietin-2 interactions with its receptor Tie2
Q81922252	Residue-wise conformational stability of DLC8 dimer from native-state hydrogen exchange
Q42079214	Resolution-adapted recombination of structural features significantly improves sampling in restraint-guided structure calculation
Q30400313	Resolving protein structure-function-binding site relationships from a binding site similarity network perspective.
Q73798394	Response to "a fast and simple method to calculate protonation states in proteins"
Q50888768	Restricted mobility of side chains on concave surfaces of solenoid proteins may impart heightened potential for intermolecular interactions
Q63391811	Retracted: Crystal structure of a Baeyer-Villiger flavin-containing monooxygenase from Staphylococcus aureus MRSA strain MU50
Q63391828	Retracted: Site-specific recombination of nitrogen-fixation genes in cyanobacteria by XisF-XisH-XisI complex: Structures and models
Q27684940	Retraction: Crystal structure of a Baeyer-Villiger flavin-containing monooxygenase from Staphylococcus aureus MRSA strain MU50, William C. Hwang, Qingping Xu, Bainan Wu, Adam Godzik
Q84764405	Retraction: Open and closed conformations reveal induced fit movements in butyrate kinase 2 activation. J. Diao, Y. D. Ma, and M. S. Hasson
Q27694941	Retraction: Site‐specific recombination of nitrogen‐fixation genes in cyanobacteria by XisF–XisH–XisI complex: Structures and models, William C. Hwang, James W. Golden, Jaime Pascual, Dong Xu, Anton Cheltsov, Adam Godzik
Q81699466	Reversal of some viral IL-6 electrostatic properties compared to IL-6 contributes to a loss of alpha receptor component recruitment
Q93069215	Reversible control of enzyme-inhibitor interactions with light illumination using a photoresponsive surfactant
Q27636882	Reversible substrate-induced domain motions in ribonuclease A
Q50668645	Review of the fifth annual Johns Hopkins Protein Folding Meeting
Q33689031	Review of the fourth Johns Hopkins protein folding meeting
Q50691129	Review of the sixth Annual Johns Hopkins Folding Meeting
Q27676233	Revised 2.3 A structure of porcine pepsin: evidence for a flexible subdomain
Q42750175	Revisiting gap locations in amino acid sequence alignments and a proposal for a method to improve them by introducing solvent accessibility
Q43825549	Revisiting the structural flexibility of the complex p21(ras)-GTP: the catalytic conformation of the molecular switch II.
Q46167124	Rhesus macaque: a tight homodimeric CD8alphaalpha
Q60639614	RhoB can adopt a Mg2+free conformation prior to GEF binding
Q45244947	Ribosome-inhibiting proteins, retroviral reverse transcriptases, and RNase H share common structural elements
Q38350098	Ricin A-chain structural determinant for binding substrate analogues: a molecular dynamics simulation analysis
Q45940899	Right- and left-handed three-helix proteins. II. Similarity and differences in mechanical unfolding of proteins
Q45820715	Right‐ and left‐handed three‐helix proteins. I. Experimental and simulation analysis of differences in folding and structure
Q42643258	Rigid body essential X-ray crystallography: distinguishing the bend and twist of glutamate receptor ligand binding domains
Q46985984	Rigid domains in proteins: an algorithmic approach to their identification
Q52386621	Rigid-body docking with mutant constraints of influenza hemagglutinin with antibody HC19.
Q43286522	RigidFinder: a fast and sensitive method to detect rigid blocks in large macromolecular complexes
Q90737631	Rigidity and flexibility characteristics of DD[E/D]-transposases Mos1 and Sleeping Beauty
Q51134435	Rigidity loss of protein macromolecule induced by force--effective field theory
Q47966241	Rigid‐body motions of interacting proteins dominate multispecific binding of ubiquitin in a shape‐dependent manner
Q50850517	Rings and ribbons in protein structures: Characterization using helical parameters and Ramachandran plots for repeating dipeptides.
Q45936094	Robustness and generalization of structure-based models for protein folding and function.
Q47711974	Role of AP-endonuclease (Ape1) active site residues in stabilization of the reactant enzyme-DNA complex
Q44125130	Role of C-terminal region of Staphylococcal nuclease for foldability, stability, and activity
Q74460966	Role of Ca(2+) for the mechanical properties of fibrillin
Q38795554	Role of N-glycosylation in EGFR ectodomain ligand binding
Q51602379	Role of W181 in modulating kinetic properties of Plasmodium falciparum hypoxanthine guanine xanthine phosphoribosyltransferase.
Q53401736	Role of active-site residues Tyr55 and Tyr114 in catalysis and substrate specificity of Corynebacterium diphtheriae C-S lyase
Q83264889	Role of amino acid hydrophobicity, aromaticity, and molecular volume on IAPP(20-29) amyloid self-assembly
Q27635356	Role of amino acid residues in left-handed helical conformation for the conformational stability of a protein
Q36866174	Role of aromatic amino acids in carbohydrate binding of plant lectins: laser photo chemically induced dynamic nuclear polarization study of hevein domain-containing lectins
Q44403947	Role of beta-lactam carboxyl group on binding of penicillins and cephalosporins to class C beta-lactamases.
Q30399243	Role of conformational sampling in computing mutation-induced changes in protein structure and stability
Q54702386	Role of conserved proline residues in stabilizing tryptophan synthase alpha subunit: analysis by mutants with alanine or glycine.
Q85076964	Role of different β‐turns in β‐hairpin conformation and stability studied by optical spectroscopy
Q82209827	Role of disulfide bonds in modulating internal motions of proteins to tune their function: molecular dynamics simulation of scorpion toxin Lqh III
Q84193469	Role of electrostatic interactions for the stability and folding behavior of cold shock protein
Q73427991	Role of electrostatics at the catalytic metal binding site in xylose isomerase action: Ca(2+)-inhibition and metal competence in the double mutant D254E/D256E
Q52209259	Role of evolutionary information in predicting the disulfide-bonding state of cysteine in proteins
Q57809406	Role of evolutionary information in predicting the disulfide-bonding state of cysteine in proteins
Q88565361	Role of glycans in cholesteryl ester transfer protein revealed by molecular dynamics simulation
Q57961910	Role of histidine for charge regulation of unstructured peptides at interfaces and in bulk
Q61758591	Role of histidine-50, glutamic acid-96, and histidine-137 in the ribonucleolytic mechanism of the ribotoxin ?-sarcin
Q73256229	Role of histidine-50, glutamic acid-96, and histidine-137 in the ribonucleolytic mechanism of the ribotoxin alpha-sarcin
Q43947462	Role of hydrophilic and hydrophobic contacts in folding of the second beta-hairpin fragment of protein G: molecular dynamics simulation studies of an all-atom model
Q73403645	Role of hydrophobic interactions in yeast phosphoglycerate kinase stability
Q79416219	Role of intrinsic disorder in transient interactions of hub proteins
Q57831583	Role of lysine versus arginine in enzyme cold-adaptation: Modifying lysine to homo-arginine stabilizes the cold-adapted α-amylase from Pseudoalteramonas haloplanktis
Q73233228	Role of metal ions on the secondary and quaternary structure of alkaline phosphatase from bovine intestinal mucosa
Q27633257	Role of non-glycine residues in left-handed helical conformation for the conformational stability of human lysozyme
Q42496692	Role of partial protein unfolding in alcohol-induced protein aggregation
Q46808448	Role of phosphorylated Thr160 for the activation of the CDK2/Cyclin A complex
Q52061433	Role of phosphorylation in conformational adaptability of bovine myelin basic protein
Q47596279	Role of protein in the primary step of the photoreaction of yellow protein
Q30431036	Role of quaternary structure in muscle creatine kinase stability: Tryptophan 210 is important for dimer cohesion
Q74449642	Role of stabilization centers in 4 helix bundle proteins
Q28205100	Role of the 14-3-3 C-terminal loop in ligand interaction
Q57135178	Role of the C-terminal chain in human interferongamma stability: an electrostatic study
Q81544588	Role of the IXI/V motif in oligomer assembly and function of StHsp14.0, a small heat shock protein from the acidothermophilic archaeon, Sulfolobus tokodaii strain 7
Q47595747	Role of the amino acid sequence in domain swapping of the B1 domain of protein G.
Q43676078	Role of the carboxy-termini of tubulin on its chaperone-like activity
Q80752686	Role of the individual domains of translation termination factor eRF1 in GTP binding to eRF3
Q41736273	Role of the minor energetic determinants of chicken egg white lysozyme (HEWL) to the stability of the HEWL.antibody scFv-10 complex
Q78627294	Role of the protein side-chain fluctuations on the strength of pair-wise electrostatic interactions: comparing experimental with computed pK(a)s
Q30349989	Role of trehalose and heat in the structure of the C-terminal activation domain of the heat shock transcription factor.
Q46327659	Role of tyrosine hot-spot residues at the interface of colicin E9 and immunity protein 9: a comparative free energy simulation study
Q27765158	Role of water in plasticity, stability, and action of proteins: The crystal structures of lysozyme at very low levels of hydration
Q54376157	Roles for the two N‐terminal (β/α) modules in the folding of a (β/α)8‐barrel protein as studied by fragmentation analysis
Q83358847	Roles of conserved basic amino acid residues and activation mechanism of the hyperthermophilic aspartate racemase at high temperature
Q88314365	Roles of conserved tryptophans in trimerization of HIV-1 membrane-proximal external regions: Implications for virucidal design via alchemical free-energy molecular simulations
Q51699019	Roles of non-native hydrogen-bonding interaction in helix-coil transition of a single polypeptide as revealed by comparison between Gō-like and non-Gō models.
Q30164238	Roles of physical interactions in determining protein-folding mechanisms: molecular simulation of protein G and alpha spectrin SH3.
Q35828040	Room temperature crystal structure of the fast switching M159T mutant of the fluorescent protein dronpa
Q48604554	Rose is a rose is a rose. Especially if you're a George
Q35631597	Rosetta comparative modeling for library design: Engineering alternative inducer specificity in a transcription factor.
Q42411390	Rosetta in CAPRI rounds 13-19.
Q28218074	Rosetta in CASP4: progress in ab initio protein structure prediction
Q30336227	Rosetta predictions in CASP5: successes, failures, and prospects for complete automation.
Q28239152	RosettaDock in CAPRI rounds 6-12
Q36087081	Rotamer libraries and probabilities of transition between rotamers for the side chains in protein-protein binding
Q48540316	Rough set-based proteochemometrics modeling of G-protein-coupled receptor-ligand interactions
Q36866168	Roughness of the globular protein surface: analysis of high resolution X-ray data
Q30357624	Routes are trees: the parsing perspective on protein folding.
Q59261918	Rubredoxin refolding on nanostructured hydrophobic surfaces: Evidence for a new type of biomimetic chaperones
Q30349966	S-adenosylhomocysteine hydrolase from the archaeon Pyrococcus furiosus: biochemical characterization and analysis of protein structure by comparative molecular modeling.
Q30351474	SAM-T04: what is new in protein-structure prediction for CASP6.
Q92147458	SAXSDom: Modeling multidomain protein structures using small-angle X-ray scattering data
Q36885869	SAmBA: an interactive software for optimizing the design of biological macromolecules crystallization experiments.
Q30379024	SESAM: a relational database for structure and sequence of macromolecules.
Q50131043	SFCscore: scoring functions for affinity prediction of protein-ligand complexes.
Q30176341	SH3 domain of Bruton's tyrosine kinase can bind to proline-rich peptides of TH domain of the kinase and p120cbl
Q27704917	SH3-like motif-containing C-terminal domain of staphylococcal teichoic acid transporter suggests possible function
Q57904273	SHBG region of the anticoagulant cofactor protein S: Secondary structure prediction, circular dichroism spectroscopy, and analysis of naturally occurring mutations
Q40874513	SHBG region of the anticoagulant cofactor protein S: secondary structure prediction, circular dichroism spectroscopy, and analysis of naturally occurring mutations
Q34071261	SIDEpro: A novel machine learning approach for the fast and accurate prediction of side‐chain conformations
Q80377686	SIMPLE estimate of the free energy change due to aliphatic mutations: superior predictions based on first principles
Q51906615	SOFTDOCK application to protein-protein interaction benchmark and CAPRI.
Q61456026	SOMCD: Method for evaluating protein secondary structure from UV circular dichroism spectraAn implementation of the method presented in this article will be available online at http://somcd.geneura.org
Q52068722	SOMCD: method for evaluating protein secondary structure from UV circular dichroism spectra
Q51963681	SPARKS 2 and SP3 servers in CASP6.
Q50420712	SPIN2: Predicting sequence profiles from protein structures using deep neural networks
Q30357106	SPINFAST: using structure alignment profiles to enhance the accuracy and assess the reliability of protein side-chain modeling.
Q30352414	SPINS: a laboratory information management system for organizing and archiving intermediate and final results from NMR protein structure determinations.
Q51956848	SSALN: an alignment algorithm using structure-dependent substitution matrices and gap penalties learned from structurally aligned protein pairs
Q39685610	STITCHER: Dynamic assembly of likely amyloid and prion β-structures from secondary structure predictions
Q34568527	STRUCTFAST: protein sequence remote homology detection and alignment using novel dynamic programming and profile-profile scoring.
Q47292616	SVM-Cabins: prediction of solvent accessibility using accumulation cutoff set and support vector machine
Q30354381	SVR_CAF: an integrated score function for detecting native protein structures among decoys.
Q81892371	Sailing the route from Gaeta, Italy, to CAPRI
Q47810337	Salt bridge interactions: stability of the ionic and neutral complexes in the gas phase, in solution, and in proteins.
Q41989888	Salt bridges: Geometrically specific, designable interactions
Q45848655	Salt effects on hydrophobic-core formation in folding of a helical miniprotein studied by molecular dynamics simulations.
Q44915256	Salt or ion bridges in biological systems: a study employing quantum and molecular mechanics
Q44125117	Salt-promoted protein folding, preferential binding, or electrostatic screening?
Q39238865	Salvianolic acid B inhibits the amyloid formation of human islet amyloid polypeptide and protects pancreatic beta-cells against cytotoxicity
Q27010280	Sampling and scoring: a marriage made in heaven
Q45190627	Sampling efficiency in explicit and implicit membrane environments studied by peptide folding simulations
Q30364680	Sampling of near-native protein conformations during protein structure refinement using a coarse-grained model, normal modes, and molecular dynamics simulations.
Q27646968	Sampling of the native conformational ensemble of myoglobin via structures in different crystalline environments
Q46030052	Sampling‐based exploration of folded state of a protein under kinematic and geometric constraints
Q46824452	Sann: Solvent accessibility prediction of proteins by nearest neighbor method
Q30372465	Satisfaction of hydrogen-bonding potential influences the conservation of polar sidechains.
Q44947544	Saturation transfer difference (STD) 1H-NMR experiments and in silico docking experiments to probe the binding of N-acetylneuraminic acid and derivatives to Vibrio cholerae sialidase
Q33920753	ScaffoldSeq: Software for characterization of directed evolution populations
Q91327241	Scalable remote homology detection and fold recognition in massive protein networks
Q47864113	Scaling law in sizes of protein sequence families: from super-families to orphan genes
Q60429766	Scan2S: Increasing the precision of PROSITE pattern motifs using secondary structure constraints
Q46115863	Score_set: a CAPRI benchmark for scoring protein complexes
Q28299530	Scoring a diverse set of high-quality docked conformations: a metascore based on electrostatic and desolvation interactions
Q52077262	Scoring docked conformations generated by rigid-body protein-protein docking
Q51970495	Scoring docking models with evolutionary information
Q30360854	Scoring function accuracy for membrane protein structure prediction.
Q29615862	Scoring function for automated assessment of protein structure template quality
Q42257042	Scoring protein interaction decoys using exposed residues (SPIDER): a novel multibody interaction scoring function based on frequent geometric patterns of interfacial residues
Q34733455	Scoring residue conservation
Q77314228	Screening a peptidyl database for potential ligands to proteins with side-chain flexibility
Q46969540	Screening of the active site from water by the incoming ligand triggers catalysis and inhibition in serine proteases
Q40760191	Search for the most stable folds of protein chains: III. Improvement in fold recognition by averaging over homologous sequences and 3D structures
Q41705448	Searching for frameshift evolutionary relationships between protein sequence families
Q51263617	Searching for protein signatures using a multilevel alphabet
Q46568963	Searching for protein-protein interaction sites and docking by the methods of molecular dynamics, grid scoring, and the pairwise interaction potential of amino acid residues
Q78315762	Searching for quantitative entropy-enthalpy compensation among protein variants
Q30419948	Searching protein structure databases has come of age.
Q46914372	Second antibody modeling assessment (AMA-II).
Q50085735	Second step of hydrolytic dehalogenation in haloalkane dehalogenase investigated by QM/MM methods
Q69658333	Second virial coefficient of alpha-crystallin
Q44630774	Secondary structural analysis of retrovirus integrase: characterization by circular dichroism and empirical prediction methods
Q72890876	Secondary structural features of modules M2 and M3 of barnase in solution by NMR experiment and distance geometry calculation
Q52364824	Secondary structural predictions for the clostridial neurotoxins
Q38629281	Secondary structure and dynamics study of the intrinsically disordered silica-mineralizing peptide P5 S3 during silicic acid condensation and silica decondensation.
Q79502796	Secondary structure length as a determinant of folding rate of proteins with two- and three-state kinetics
Q46217877	Secondary structure prediction and unrefined tertiary structure prediction for cyclin A, B, and D.
Q30195749	Secondary structure-based profiles: use of structure-conserving scoring tables in searching protein sequence databases for structural similarities
Q27687161	Secondary sugar binding site identified for LecA lectin from Pseudomonas aeruginosa
Q44245143	Secondary‐structure analysis of alcohol‐denatured proteins by vacuum‐ultraviolet circular dichroism spectroscopy
Q40861289	Secretion of cytoplasmic and nuclear proteins from animal cells using novel secretion modules
Q46464609	Segment swapping aided the evolution of enzyme function: The case of uroporphyrinogen III synthase
Q53529546	Selected-fit versus induced-fit protein binding: kinetic differences and mutational analysis
Q30757774	Selection and affinity maturation of IgNAR variable domains targeting Plasmodium falciparum AMA1.
Q33191653	Selection of a representative set of structures from Brookhaven Protein Data Bank
Q41840576	Selection of near-native poses in CAPRI rounds 13-19.
Q30377216	Selective refinement and selection of near-native models in protein structure prediction.
Q40469351	Selective targeting of indel-inferred differences in spatial structures of highly homologous proteins.
Q48046292	Self-assembling study of sarcolipin and its mutants in multiple molecular dynamic simulations.
Q27661466	Self-association of TPR domains: Lessons learned from a designed, consensus-based TPR oligomer
Q77771924	Self-consistent estimation of inter-residue protein contact energies based on an equilibrium mixture approximation of residues
Q30427177	Self-consistent field approach to protein structure and stability. I: pH dependence of electrostatic contribution
Q42198361	Self-guided Langevin dynamics study of regulatory interactions in NtrC.
Q45736470	Self-repair of biological fibers catalyzed by the surface of a virus crystal
Q50878481	Sense and Simplicity in HADDOCK Scoring: Lessons from CASP-CAPRI (page 418).
Q37664304	Sense and simplicity in HADDOCK scoring: Lessons from CASP-CAPRI round 1.
Q51611817	Sensing the dissociation of a polymeric enzyme by means of an engineered intrinsic probe
Q50482715	Sensitive detection of sequence similarity using combinatorial pattern discovery: a challenging study of two distantly related protein families
Q44526586	Separability between overall and internal motion: A protein folding problem
Q50909018	Separating true positive predicted residue contacts from false positive ones in mainly alpha proteins, using constrained Metropolis MC simulations.
Q73792004	Sequence analysis reveals how G protein-coupled receptors transduce the signal to the G protein
Q85639676	Sequence and conformational preferences at termini of α-helices in membrane proteins: role of the helix environment
Q40541100	Sequence and structural analysis of cellular retinoic acid-binding proteins reveals a network of conserved hydrophobic interactions
Q57829327	Sequence and structural determinants of Cu, Zn superoxide dismutase aggregation
Q73798374	Sequence and structural determinants of mannose recognition
Q57752885	Sequence and structural features of the T-fold, an original tunnelling building unit
Q45876582	Sequence and structural properties of identical mutations with varying phenotypes in human coagulation factor IX.
Q77603395	Sequence and structure conservation in a protein core
Q46868110	Sequence and structure of epoxide hydrolases: a systematic analysis
Q92926943	Sequence and structure-based characterization of ubiquitination sites in human and yeast proteins using Chou's sample formulation
Q73380001	Sequence codes for extended conformation: a neighbor-dependent sequence analysis of loops in proteins
Q29616420	Sequence complexity of disordered protein
Q70388091	Sequence conservation and region shuffling in an endoglucanase and an exoglucanase from Cellulomonas fimi
Q44078752	Sequence determinants of protein architecture
Q47720602	Sequence determinants of protein folding rates: positive correlation between contact energy and contact range indicates selection for fast folding
Q27657531	Sequence fingerprint and structural analysis of the SCOR enzyme A3DFK9 from Clostridium thermocellum
Q62660449	Sequence patterns associated with disordered regions in proteins
Q42139934	Sequence recombination improves target specificity in a redesigned collagen peptide abc-type heterotrimer
Q73094556	Sequence to structure alignment in comparative modeling using PrISM
Q38761956	Sequence-based analysis of protein degradation rates.
Q80610312	Sequence-based prediction of pathological mutations
Q51903855	Sequence-based protein domain boundary prediction using BP neural network with various property profiles
Q57953580	Sequence-based study of two related proteins with different folding behaviors
Q30365843	Sequence-similar, structure-dissimilar protein pairs in the PDB.
Q92331496	Sequence-specific dynamic information in proteins
Q30329569	Sequence-structure homology recognition by iterative alignment refinement and comparative modeling.
Q42641933	Sequence-structure-function analysis of the bifunctional enzyme MnmC that catalyses the last two steps in the biosynthesis of hypermodified nucleoside mnm5s2U in tRNA.
Q46403152	Sequence-structure-function relationships of a tRNA (m7G46) methyltransferase studied by homology modeling and site-directed mutagenesis
Q39618799	Sequential four‐state folding/unfolding of goat α‐lactalbumin and its N‐terminal variants
Q79375667	Serendipitous discovery of novel bacterial methionine aminopeptidase inhibitors
Q73393602	Serine proteases: an ab initio molecular dynamics study
Q77894285	Serpins in the Caenorhabditis elegans genome
Q58023165	Serpins in theCaenorhabditis elegans genome
Q39699460	Set of novel, conserved proteins fold pre-messenger RNA into ribonucleosomes
Q81489821	Seventh Meeting on the Critical Assessment of Techniques for Protein Structure Prediction
Q38558729	Seventy-five percent accuracy in protein secondary structure prediction
Q30380400	Shape and evolution of thermostable protein structure.
Q41837120	Shape complementarity of protein-protein complexes at multiple resolutions
Q43729912	Shape evolution with temperature of a thermotolerant protein (PeaT1) in solution detected by small angle X‐ray scattering
Q27648760	Shark IgNAR antibody mimotopes target a murine immunoglobulin through extended CDR3 loop structures
Q51772435	Shelling the Voronoi interface of protein-protein complexes reveals patterns of residue conservation, dynamics, and composition.
Q44947532	Shift in nucleotide conformational equilibrium contributes to increased rate of catalysis of GpAp versus GpA in barnase
Q47626873	Short-range conformational energies, secondary structure propensities, and recognition of correct sequence-structure matches
Q30009100	Shortening a loop can increase protein native state entropy.
Q48053109	Shuffling of structural elements in filamentous bacteriophages
Q39032562	Side chain flexibility and coupling between the S4-S5 linker and the TRP domain in thermo-sensitive TRP channels: Insights from protein modeling
Q90267317	Side chain rotameric changes and backbone dynamics enable specific cladosporin binding in Plasmodium falciparum lysyl-tRNA synthetase
Q41161629	Side chain-backbone hydrogen bonding contributes to helix stability in peptides derived from an alpha-helical region of carboxypeptidase A.
Q73912098	Side chains in transmembrane helices are shorter at helix-helix interfaces
Q73912102	Side-chain conformational entropy in protein unfolded states
Q30333120	Side-chain dynamics and protein folding.
Q81546937	Side-chain entropy effects on protein secondary structure formation
Q52080522	Side-chain flexibility in proteins upon ligand binding
Q51667050	Side-chain rotamer transitions at protein-protein interfaces
Q44060650	Signal transduction in the photoactive yellow protein. I. Photon absorption and the isomerization of the chromophore
Q44060653	Signal transduction in the photoactive yellow protein. II. Proton transfer initiates conformational changes
Q83319473	Signaling pathway of a photoactivable Rac1-GTPase in the early stages
Q37019487	Signaling pathways of PDZ2 domain: a molecular dynamics interaction correlation analysis
Q83319611	Signatures of the ATP-binding pocket as a basis for structural classification of the serine/threonine protein kinases of gram-positive bacteria
Q30328185	Significance of aromatic-backbone amide interactions in protein structure.
Q33206312	Significance of conformational biases in Monte Carlo simulations of protein folding: lessons from Metropolis-Hastings approach.
Q34273201	Silk fibroin: structural implications of a remarkable amino acid sequence.
Q30351841	SimFold energy function for de novo protein structure prediction: consensus with Rosetta.
Q30367656	Similar chemistry, but different bond preferences in inter versus intra-protein interactions.
Q51959646	Similarity networks of protein binding sites
Q42975911	Similarity of cytochrome c oxidases in different organisms
Q52076419	Similarity-driven flexible ligand docking
Q30692839	Simple sequences are rare in the Protein Data Bank
Q58033010	Simple solvation potential for coarse-grained models of proteins
Q51838206	Simple two-state protein folding kinetics requires near-levinthal thermodynamic cooperativity
Q30336275	Simplicial edge representation of protein structures and alpha contact potential with confidence measure.
Q101211221	Simplified geometric representations of protein structures identify complementary interaction interfaces
Q42712396	Simplified modeling approach suggests structural mechanisms for constitutive activation of the C5a receptor
Q80546575	Simulated annealing exploration of an active-site tyrosine in TEM-1 beta-lactamase suggests the existence of alternate conformations
Q34820098	Simulated tempering yields insight into the low-resolution Rosetta scoring functions
Q45964522	Simulating electrostatic energies in proteins: perspectives and some recent studies of pKas, redox, and other crucial functional properties.
Q43166561	Simulating protein folding initiation sites using an alpha-carbon-only knowledge-based force field
Q52040919	Simulating proteins at constant pH: An approach combining molecular dynamics and Monte Carlo simulation
Q41685643	Simulating proton translocations in proteins: probing proton transfer pathways in the Rhodobacter sphaeroides reaction center
Q46108702	Simulating the fidelity and the three Mg mechanism of pol η and clarifying the validity of transition state theory in enzyme catalysis
Q52908895	Simulation of peptide folding with explicit water--a mean solvation method
Q73319277	Simulation of protein conformational freedom as a function of pH: constant-pH molecular dynamics using implicit titration
Q46453321	Simulation of protein crystal nucleation
Q47565535	Simulation of the effect of an external GHz electric field on the potential energy profile of Ca2+ ions in the selectivity filter of the CaV Ab channel
Q39547080	Simulation of the mutation F76del on the von Hippel–Lindau tumor suppressor protein: Mechanism of the disease and implications for drug development
Q34223245	Simulation of the β‐ to α‐sheet transition results in a twisted sheet for antiparallel and an α‐nanotube for parallel strands: Implications for amyloid formation
Q73845018	Simulation of two-dimensional streptavidin crystallization
Q54509343	Simulation reveals two major docking pathways between the hexapeptide GDYMNM and the catalytic domain of the insulin receptor protein kinase.
Q46820099	Simulations of ion current in realistic models of ion channels: the KcsA potassium channel
Q35949089	Simulations of substrate transport in the multidrug transporter EmrD
Q41465545	Simultaneous prediction of protein secondary structure and transmembrane spans
Q47565056	Simultaneous refinement of inaccurate local regions and overall structure in the CASP12 protein model refinement experiment
Q34773665	Single and multiple input modules in regulatory networks
Q54735609	Single crystals of bacteriophage T7 RNA polymerase.
Q47596351	Single-body residue-level knowledge-based energy score combined with sequence-profile and secondary structure information for fold recognition
Q72685101	Single-site modifications of half-ligated hemoglobin reveal autonomous dimer cooperativity within a quaternary T tetramer
Q43796913	Single-stranded DNA binding proteins (SSBs) from prokaryotic transmissible plasmids
Q30670853	Singular value decomposition analysis of protein sequence alignment score data
Q90307982	Singular value decomposition for the correlation of atomic fluctuations with arbitrary angle
Q51917208	Site directed mutagenesis at position 193 of human trypsin 4 alters the rate of conformational change during activation: role of local internal viscosity in protein dynamics.
Q57209062	Site specific point mutation changes specificity: A molecular modeling study by free energy simulations and enzyme kinetics of the thermodynamics in ribonuclease T1 substrate interactions
Q33247198	Site-directed combinatorial construction of chimaeric genes: general method for optimizing assembly of gene fragments
Q46024915	Site-directed mutagenesis of colicin E1 provides specific attachment sites for spin labels whose spectra are sensitive to local conformation.
Q67959668	Site-directed mutagenesis of ricin A-chain and implications for the mechanism of action
Q38345575	Site-directed mutagenesis of the T4 endonuclease V gene: mutations which enhance enzyme specific activity at low salt concentrations
Q54756843	Site-directed mutations altering methyl-accepting residues of a sensory transducer protein.
Q70618658	Site-specific proteolytic cleavage of Ku protein bound to DNA
Q46873060	Site-specific transamidation and deamidation of the small heat-shock protein Hsp20 by tissue transglutaminase
Q47175786	Size determination of multienzyme complexes using two-dimensional agarose gel electrophoresis
Q47351957	Size-independent comparison of protein three-dimensional structures
Q46150489	Sizes of interface residues account for cross-class binding affinity patterns in Eph receptor-ephrin families
Q43256878	Slow formation of aggregation-resistant beta-sheet folding intermediates
Q47191421	Small angle X-ray scattering and cross-linking for data assisted protein structure prediction in CASP 12 with prospects for improved accuracy
Q90564420	Small angle X-ray scattering-assisted protein structure prediction in CASP13 and emergence of solution structure differences
Q43669505	Small cationic protein from a marine turtle has beta-defensin-like fold and antibacterial and antiviral activity
Q72074164	Small effects of amino acid replacements on the reduced and unfolded state of pancreatic trypsin inhibitor
Q52560762	Small-Angle x-ray scattering and crystallographic studies of arcelin-1: An insecticidal lectin-like glycoprotein from Phaseolus vulgaris L
Q45891411	Small-angle X-ray scattering of BAMLET at pH 12: a complex of α-lactalbumin and oleic acid.
Q44536579	Small-angle X-ray scattering reveals architecture and A₂B₂ stoichiometry of the UvrA-UvrB DNA damage sensor.
Q81193331	Small-world network approach to identify key residues in protein-protein interaction
Q85200800	Smoothing molecular interactions: The “kinetic buffer” effect of intrinsically disordered proteins
Q48254561	Soft interactions and volume exclusion by polymeric crowders can stabilize or destabilize transient structure in disordered proteins depending on polymer concentration
Q33511797	Solid-state NMR and simulation studies of equinatoxin II N-terminus interaction with lipid bilayers
Q46846379	Solubilization of cellulosomal cellulases by fusion with cellulose-binding domain of noncellulosomal cellulase engd from Clostridium cellulovorans
Q27625013	Soluble beta-galactosyl-binding lectin (galectin) from toad ovary: crystallographic studies of two protein-sugar complexes
Q30692723	Solution NMR analysis of the interaction between the actinoporin sticholysin I and DHPC micelles--correlation with backbone dynamics
Q38544515	Solution NMR and molecular dynamics reveal a persistent alpha helix within the dynamic region of PsbQ from photosystem II of higher plants
Q27675781	Solution NMR structure of Asl3597 from Nostoc sp. PCC7120, the first structure from protein domain family PF12095, reveals a novel fold
Q27675795	Solution NMR structure of BT_0084, a conjugative transposon lipoprotein from Bacteroides thetaiotamicron
Q99572378	Solution NMR structure of Borrelia burgdorferi outer surface lipoprotein BBP28, a member of the mlp protein family
Q91793224	Solution NMR structure of CGL2373, a polyketide cyclase-like protein from Corynebacterium glutamicum
Q58109481	Solution NMR structure of CHU_1110 from Cytophaga hutchinsonii, an AHSA1 protein potentially involved in metal ion stress response
Q27644873	Solution NMR structure of Escherichia coli ytfP expands the structural coverage of the UPF0131 protein domain family
Q27663104	Solution NMR structure of Lin0431 protein from Listeria innocua reveals high structural similarity with domain II of bacterial transcription antitermination protein NusG
Q47985110	Solution NMR structure of RHE_CH02687 from Rhizobium etli: A novel flavonoid-binding protein.
Q27673658	Solution NMR structure of VF0530 from Vibrio fischeri reveals a nucleic acid-binding function
Q27682474	Solution NMR structure of a sheddase inhibitor prodomain from the malarial parasite Plasmodium falciparum
Q27665632	Solution NMR structure of photosystem II reaction center protein Psb28 fromSynechocystis sp. Strain PCC 6803
Q27661470	Solution NMR structure of the ARID domain of human AT-rich interactive domain-containing protein 3A: A human cancer protein interaction network target
Q28236103	Solution NMR structure of the SH3 domain of human nephrocystin and analysis of a mutation-causing juvenile nephronophthisis
Q27650416	Solution NMR structure of the SOS response protein YnzC from Bacillus subtilis
Q27665384	Solution NMR structure of the plasmid-encoded fimbriae regulatory protein PefI fromSalmonella entericaserovar Typhimurium
Q27678059	Solution NMR structure of the ribosomal protein RP-L35Ae from Pyrococcus furiosus
Q47985123	Solution NMR structure of zinc finger 4 and 5 from human INSM1, an essential regulator of neuroendocrine differentiation.
Q27658281	Solution NMR structures of proteins VPA0419 fromVibrio parahaemolyticusand yiiS fromShigella flexneriprovide structural coverage for protein domain family PFAM 04175
Q27724656	Solution NMR structures of the C-domain of Tetrahymena cytoskeletal protein Tcb2 reveal distinct calcium-induced structural rearrangements
Q30361451	Solution NMR studies reveal no global flexibility in the catalytic domain of CDC25B.
Q27694773	Solution and crystal structure of BA42, a protein from the Antarctic bacterium Bizionia argentinensis comprised of a stand-alone TPM domain
Q27694772	Solution and high-pressure NMR studies of the structure, dynamics, and stability of the cross-reactive allergenic cod parvalbumin Gad m 1
Q27619420	Solution structure and RNA-binding activity of the N-terminal leucine-repeat region of hepatitis delta antigen
Q27638952	Solution structure and backbone dynamics of an antigen-free heavy chain variable domain (VHH) from Llama
Q82490286	Solution structure and binding specificity of FBP11/HYPA WW domain as Group-II/III
Q27657489	Solution structure and calcium binding of protein SSO6904 from the hyperthermophilic archaeon Sulfolobus solfataricus
Q27658668	Solution structure and dynamics of human ubiquitin conjugating enzyme Ube2g2
Q27633250	Solution structure and dynamics of ribonuclease Sa
Q33684835	Solution structure and function of YndB, an AHSA1 protein from Bacillus subtilis
Q27654532	Solution structure and glycophorin C binding studies of the protein 4.1R FERM alpha-lobe domain
Q27687513	Solution structure and interface-driven self-assembly of NC2, a new member of the Class II hydrophobin proteins
Q51575984	Solution structure and interface-driven self-assembly of NC2, a new member of the Class II hydrophobin proteins
Q27649056	Solution structure and neutralizing antibody binding studies of domain III of the dengue-2 virus envelope protein
Q30373528	Solution structure and properties of AlgH from Pseudomonas aeruginosa.
Q27681815	Solution structure and siRNA-mediated knockdown analysis of the mitochondrial disease-related protein C12orf65
Q27679209	Solution structure and small angle scattering analysis of TraI (381–569)
Q27642856	Solution structure of ADO1, a toxin extracted from the saliva of the assassin bug, Agriosphodrus dohrni
Q45279390	Solution structure of APETx1 from the sea anemone Anthopleura elegantissima: a new fold for an HERG toxin
Q27643665	Solution structure of ApaG from Xanthomonas axonopodis pv. citri reveals a fibronectin-3 fold
Q27654551	Solution structure of Apo-YjaB from Escherichia coli
Q27649618	Solution structure of At3g28950 fromArabidopsis thaliana
Q34321170	Solution structure of BmKK2, a new potassium channel blocker from the venom of chinese scorpion Buthus martensi Karsch
Q27621087	Solution structure of BmKTX, a K+ blocker toxin from the Chinese scorpion Buthus Martensi
Q27648246	Solution structure of FK506 binding domain (FKBD) of Plasmodium falciparum FK506 binding protein 35 (PfFKBP35)
Q27681771	Solution structure of FK506-binding protein 12 from Aedes aegypti
Q53611841	Solution structure of HP1242 from Helicobacter pylori
Q27666898	Solution structure of MTH1821, a putative structure homologue to RNA polymerase α subunit from Methanobacterium thermoautotrophicum
Q27733317	Solution structure of P01, a natural scorpion peptide structurally analogous to scorpion toxins specific for apamin-sensitive potassium channel
Q27654550	Solution structure of SUMO from Trypanosoma brucei and its interaction with Ubc9
Q27678405	Solution structure of SWI1 AT‐rich interaction domain from Saccharomyces cerevisiae and its nonspecific binding to DNA
Q58002371	Solution structure of TA0895, a MoaD homologue from Thermoplasma acidophilum
Q58002372	Solution structure of TA1092, a ribosomal protein S24e from Thermoplasma acidophilum
Q27704293	Solution structure of TbTFIIS2-1 PWWP domain from Trypanosoma brucei
Q27747236	Solution structure of TsKapa, a charybdotoxin-like scorpion toxin fromTityus serrulatus with high affinity for apamin-sensitive Ca2+-activated K+ channels
Q27653941	Solution structure of Urm1 from Trypanosoma brucei
Q50085322	Solution structure of YggX: a prokaryotic protein involved in Fe(II) trafficking
Q27696171	Solution structure of a bacterial immunoglobulin-like domain of the outer membrane protein (LigB) from Leptospira
Q46442047	Solution structure of a core peptide derived from scyllatoxin
Q73403635	Solution structure of a peptide model of a region important for the folding of alpha-lactalbumin provides evidence for the formation of nonnative structure in the denatured state
Q38330231	Solution structure of a tobacco lipid transfer protein exhibiting new biophysical and biological features
Q67302272	Solution structure of a zinc finger domain of yeast ADR1
Q58002375	Solution structure of acyl carrier protein from Nitrosomonas europaea
Q27648880	Solution structure of conserved hypothetical protein HP0892 from Helicobacter pylori
Q81364388	Solution structure of conserved hypothetical protein HP0894 from Helicobacter pylori
Q45076939	Solution structure of gamma-bungarotoxin: the functional significance of amino acid residues flanking the RGD motif in integrin binding
Q27675489	Solution structure of gp17 from the Siphoviridae bacteriophage SPP1: insights into its role in virion assembly
Q27649603	Solution structure of human DESR1, a CSL zinc-binding protein
Q54440866	Solution structure of human calcitonin in membrane-mimetic environment: The role of the amphipathic helix
Q34533326	Solution structure of human erythroid p55 PDZ domain
Q44910185	Solution structure of hypothetical Nudix hydrolase DR0079 from extremely radiation-resistant Deinococcus radiodurans bacterium
Q27653394	Solution structure of hypothetical protein HP1423 (Y1423_HELPY) reveals the presence of alphaL motif related to RNA binding
Q27644151	Solution structure of hypothetical protein, HP0495 (Y495_HELPY) from Helicobacter pylori
Q27747214	Solution structure of maurotoxin, a scorpion toxin from Scorpio maurus, with high affinity for voltage-gated potassium channels
Q27617577	Solution structure of potassium channel-inhibiting scorpion toxin Lq2
Q27731512	Solution structure of tertiapin determined using nuclear magnetic resonance and distance geometry
Q27655529	Solution structure of the AT-rich interaction domain of Jumonji/JARID2
Q27661476	Solution structure of the C-terminal DUF1000 domain of the human thioredoxin-like 1 protein
Q27653397	Solution structure of the C-terminal domain of multiprotein bridging factor 1 (MBF1) of Trichoderma reesei
Q27728175	Solution structure of the Cys74 to Ala74 mutant of the recombinant catalytic domain of Zoocin A
Q27655402	Solution structure of the DNA binding domain of AraC protein
Q24313587	Solution structure of the DNA-binding domain of interleukin enhancer binding factor 1 (FOXK1a)
Q27654184	Solution structure of the Escherichia coli HybE reveals a novel fold
Q27651114	Solution structure of the GUCT domain from human RNA helicase II/Gu beta reveals the RRM fold, but implausible RNA interactions
Q27660307	Solution structure of the N-terminal domain of Bacillus subtilis delta subunit of RNA polymerase and its classification based on structural homologs
Q27651937	Solution structure of the Pseudomonas putida protein PpPutA45 and its DNA complex
Q27683597	Solution structure of the SH3 domain of DOCK180
Q27649053	Solution structure of the beta-subunit of the translation initiation factor aIF2 from archaebacteria Sulfolobus solfataricus
Q40821561	Solution structure of the calmodulin-like C-terminal domain of Entamoeba α-actinin2.
Q27657259	Solution structure of the fourth FF domain of yeast Prp40 splicing factor
Q27643051	Solution structure of the highly acidic protein HI1450 from Haemophilus influenzae, a putative double-stranded DNA mimic
Q27646762	Solution structure of the hypothetical novel-fold protein TA0956 from Thermoplasma acidophilum
Q27657137	Solution structure of the inhibitory phosphorylation domain of myosin phosphatase targeting subunit 1
Q27706695	Solution structure of the lymphocyte receptor Nkrp1a reveals a distinct conformation of the long loop region as compared to in the crystal structure
Q46093665	Solution structure of the plant defensin VrD1 from mung bean and its possible role in insecticidal activity against bruchids
Q27667655	Solution structure of the protein lipocalin 12 from rat epididymis
Q27683516	Solution structure of the recombinant target recognition domain of zoocin A
Q27666896	Solution structure of the second PDZ domain of Zonula Occludens 1
Q57893966	Solution structure of the splicing factor motif of the human Prp18 protein
Q44784468	Solution structure of the ubiquitin-binding domain in Swa2p from Saccharomyces cerevisiae
Q27650761	Solution structure of the yeast URN1 splicing factor FF domain: comparative analysis of charge distributions in FF domain structures-FFs and SURPs, two domains with a similar fold
Q34396834	Solution structure of two insect-specific spider toxins and their pharmacological interaction with the insect voltage-gated Na+ channel
Q42232132	Solution structure studies of monomeric human TIP47/perilipin-3 reveal a highly extended conformation.
Q27652347	Solution structures and DNA binding properties of the N-terminal SAP domains of SUMO E3 ligases from Saccharomyces cerevisiae and Oryza sativa
Q27675444	Solution structures of Mycobacterium tuberculosis thioredoxin C and models of intact thioredoxin system suggest new approaches to inhibitor and drug design
Q27638108	Solution structures of a 30-residue amino-terminal domain of the carp granulin-1 protein and its amino-terminally truncated 3-30 subfragment: implications for the conformational stability of the stack of two beta-hairpins
Q27666630	Solution structures of chicken parvalbumin 3 in the Ca(2+)-free and Ca(2+)-bound states
Q27682468	Solution structures of polcalcin Phl p 7 in three ligation states: Apo-, hemi-Mg2+-bound, and fully Ca2+-bound
Q27678235	Solution structures of the double-stranded RNA-binding domains from RNA helicase A
Q83880394	Solution structures of the first and fourth TSR domains of F-spondin
Q46741111	Solution structures of the reduced and Cu(I) bound forms of the first metal binding sequence of ATP7A associated with Menkes disease
Q27664077	Solution structures of the trihelix DNA-binding domains of the wild-type and a phosphomimetic mutant of Arabidopsis GT-1: mechanism for an increase in DNA-binding affinity through phosphorylation
Q27644210	Solution structures, dynamics, and lipid-binding of the sterile alpha-motif domain of the deleted in liver cancer 2
Q55120528	Solvated protein-protein docking using Kyte-Doolittle-based water preferences
Q46084222	Solvation energy density occlusion approximation for evaluation of desolvation penalties in biomolecular interactions
Q80947725	Solvation influences flap collapse in HIV-1 protease
Q40594020	Solvation parameters for predicting the structure of surface loops in proteins: Transferability and entropic effects
Q52077724	Solvent density and long-range dipole field around a DNA-binding protein studied by molecular dynamics
Q58008886	Solvent effects in the slow dynamics of proteins
Q38317707	Solvent participation in Serratia marcescens endonuclease complexes
Q58622068	Solvent polarity-dependent structural refolding: A CD and NMR study of a 15 residue peptide
Q73205387	Solvent structure at a hydrophobic protein surface
Q44121797	Solvent structure in crystals of trypsin determined by X-ray and neutron diffraction
Q44898270	Solvent-accessible surface area: How well can be applied to hot-spot detection?
Q27649298	Solvent-exposed residues located in the beta-sheet modulate the stability of the tetramerization domain of p53--a structural and combinatorial approach
Q34317861	Solvent-induced organization: a physical model of folding myoglobin
Q33946823	Some insights into protein structural class prediction
Q30323189	Some measures of comparative performance in the three CASPs.
Q30380342	Some of the most interesting CASP11 targets through the eyes of their authors
Q40242791	Some recommendations for the practitioner to improve the precision of experimentally determined protein folding rates and phi values
Q51040720	Sop-GPU: accelerating biomolecular simulations in the centisecond timescale using graphics processors.
Q41644075	Sparse networks of directly coupled, polymorphic, and functional side chains in allosteric proteins
Q38128264	Sparsely populated residue conformations in protein structures: Revisiting “experimental” Ramachandran maps
Q47683971	Spatial features of proteins related to their phosphorylation and associated structural changes
Q51651767	Spatial optimization of electrostatic interactions between the ionized groups in globular proteins
Q47700042	Spatial profiling of protein hydrophobicity: native vs. decoy structures
Q30383922	Spatial proximity statistics suggest a regulatory role of protein phosphorylation on compound binding.
Q78136332	Special issue dedicated to Herman Berendsen: researcher, teacher, scholar, colleague, skipper
Q47974598	Species dependence of enzyme-substrate encounter rates for triose phosphate isomerases
Q35110256	Species specificity of the complement inhibitor compstatin investigated by all-atom molecular dynamics simulations
Q73964877	Species-specificity of the cohesin-dockerin interaction betweenClostridium thermocellum andClostridium cellulolyticum: Prediction of specificity determinants of the dockerin domain
Q82920335	Specific DNA binding by the homeodomain Nkx2.5(C56S): detection of impaired DNA or unfolded protein by isothermal titration calorimetry
Q30968418	Specific DNA recognition by the Antp homeodomain: MD simulations of specific and nonspecific complexes
Q74267471	Specific fluorescent labeling of two functional domains in RNA polymerase α subunit
Q74177414	Specific interaction of cytosolic and mitochondrial glyoxalase II with acidic phospholipids in form of liposomes results in the inhibition of the cytosolic enzyme only
Q51893728	Specific interactions for ab initio folding of protein terminal regions with secondary structures
Q30388325	Specific interactions of sticholysin I with model membranes: an NMR study.
Q27690648	Specific potassium ion interactions facilitate homocysteine binding to betaine-homocysteine S-methyltransferase
Q27666846	Specificity and cooperativity at β‐lactamase position 104 in TEM‐1/BLIP and SHV‐1/BLIP interactions
Q42547719	Specificity in structure-based drug design: Identification of a novel, selective inhibitor of Pneumocystis carinii dihydrofolate reductase
Q42876442	Specificity of a protein-protein interface: local dynamics direct substrate recognition of effector caspases
Q47171755	Specificity of a protein–protein interface: Local dynamics direct substrate recognition of effector caspases
Q31117244	Specificity of helix packing in transmembrane dimer of the cell death factor BNIP3: a molecular modeling study
Q58898186	Specificity of molecular interactions in transient protein-protein interaction interfaces
Q27652870	Spectroscopic and crystallographic studies of the mutant R416W give insight into the nucleotide binding traits of subunit B of the A1Ao ATP synthase
Q46303556	Spectroscopic evidence for preexisting T- and R-state insulin hexamer conformations
Q79320555	Spectroscopic study of conformational changes accompanying self-assembly of HCV core protein
Q46093766	Speeding protein folding beyond the Gō model: How a little frustration sometimes helps
Q44745632	Splice variants: a homology modeling approach
Q27649627	Spontaneous asparaginyl deamidation of canine milk lysozyme under mild conditions
Q57752464	Spontaneous beta-barrel formation: an all-atom Monte Carlo study of Abeta16-22 oligomerization
Q62001994	Spontaneous β-helical fold in prion protein: The case of PrP(82-146)
Q48007473	Squeezed exponential kinetics to describe a nonglassy downhill folding as observed in a lattice protein model
Q73403638	Stability analysis for the cavity-filling mutations of the Myb DNA-binding domain utilizing free-energy calculations
Q42164198	Stability and conformational dynamics of metallothioneins from the antarctic fish Notothenia coriiceps and mouse.
Q30176728	Stability and folding of the SH3 domain of Bruton's tyrosine kinase
Q54163512	Stability of TEM beta-lactamase mutants hydrolyzing third generation cephalosporins
Q46293353	Stability of macromolecular complexes
Q77669589	Stability of secondary structural elements in a solvent-free environment. II: the beta-pleated sheets
Q73134798	Stability of secondary structural elements in a solvent-free environment: the alpha helix
Q88781957	Stability of structurally entangled protein dimers
Q46714320	Stability of wild-type and mutant RTEM-1 beta-lactamases: effect of the disulfide bond
Q58041733	Stability scale and atomic solvation parameters extracted from 1023 mutation experiments
Q50772668	Stability strengths and weaknesses in protein structures detected by statistical potentials: Application to bovine seminal ribonuclease
Q27649146	Stabilization of antibody structure upon association to a human carbonic anhydrase IX epitope studied by X-ray crystallography, microcalorimetry, and molecular dynamics simulations
Q38350564	Stabilization of lambda repressor against thermal denaturation by site-directed Gly----Ala changes in alpha-helix 3.
Q42269421	Stabilization of the integrase-DNA complex by Mg2+ ions and prediction of key residues for binding HIV-1 integrase inhibitors.
Q57139038	Stabilization of the ribonuclease S-peptide alpha-helix by trifluoroethanol
Q92372207	Stabilization of μ-opioid receptor facilitates its cellular translocation and signaling
Q31709878	Stabilizing C-terminal tails on AraC.
Q43825567	Stabilizing nonpolar/polar side-chain interactions in the alpha-helix
Q44041127	Stacking efficiency and flexibility analysis of aromatic amino acids in cap-binding proteins.
Q79969456	Starch-synthase III family encodes a tandem of three starch-binding domains
Q30577861	Starting‐structure dependence of nanosecond timescale intersubstate transitions and reproducibility of MD‐derived order parameters
Q56877658	Static and dynamic water molecules in Cu,Zn superoxide dismutase
Q46807317	Statistical analysis and prediction of protein-protein interfaces
Q91325560	Statistical analysis of disease-causing and neutral mutations in human membrane proteins
Q57814774	Statistical analysis of predominantly transient protein-protein interfaces
Q84075114	Statistical analysis of protein structures suggests that buried ionizable residues in proteins are hydrogen bonded or form salt bridges
Q41945611	Statistical analysis of structural determinants for protein-DNA-binding specificity
Q33262420	Statistical and conformational analysis of the electron density of protein side chains
Q46529625	Statistical and molecular dynamics studies of buried waters in globular proteins
Q80380712	Statistical characterization of salt bridges in proteins
Q45288456	Statistical criteria for the identification of protein active sites using Theoretical Microscopic Titration Curves
Q44935103	Statistical geometry based prediction of nonsynonymous SNP functional effects using random forest and neuro-fuzzy classifiers
Q77192762	Statistical mechanics of protein folding by exhaustive enumeration
Q30404525	Statistical mechanics‐based method to extract atomic distance‐dependent potentials from protein structures
Q30355144	Statistical potential-based amino acid similarity matrices for aligning distantly related protein sequences.
Q51639179	Statistical sequence analyses of G-protein-coupled receptors: structural and functional characteristics viewed with periodicities of entropy, hydrophobicity, and volume
Q30427190	Statistical torsion angle potential energy functions for protein structure modeling: A bicubic interpolation approach
Q73798407	Steady-state and time resolved fluorescence of albumins interacting with N-oleylethanolamine, a component of the endogenous N-acylethanolamines
Q46900608	Steady-state and time-resolved fluorescence studies of the intestinal fatty acid binding protein.
Q74614427	Steady-state fluorescence and circular dichroism of trout hemoglobins I and IV interacting with tributyltin
Q77924666	Steered molecular dynamics simulations of force-induced protein domain unfolding
Q51093482	Steiner minimal trees, twist angles, and the protein folding problem
Q33281773	Stepwise prediction of conformational discontinuous B-cell epitopes using the Mapitope algorithm
Q27860874	Stereochemical quality of protein structure coordinates
Q30356915	Stereochemistry of guanidine-metal interactions: implications for L-arginine-metal interactions in protein structure and function.
Q68082934	Stereochemistry of salt-bridge formation in alpha-helices and beta-strands
Q27729901	Steric and conformational features of the aconitase mechanism
Q35642158	Steric and thermodynamic limits of design for the incorporation of large unnatural amino acids in aminoacyl-tRNA synthetase enzymes
Q83063459	Stop-flow kinetics studies of the interaction of surfactant, sodium dodecyl sulfate, with acid-denatured cytochrome c
Q53872945	Stopped-flow NMR measurement of hydrogen exchange rates in reduced horse cytochromec under strongly destabilizing conditions
Q52206849	Strain in protein structures as viewed through nonrotameric side chains: I. their position and interaction
Q52206845	Strain in protein structures as viewed through nonrotameric side chains: II. effects upon ligand binding
Q46132517	Strand-loop-strand motifs: prediction of hairpins and diverging turns in proteins
Q30358641	Strategies for high-throughput comparative modeling: applications to leverage analysis in structural genomics and protein family organization.
Q43032317	Strategies for structural proteomics of prokaryotes: Quantifying the advantages of studying orthologous proteins and of using both NMR and X-ray crystallography approaches
Q44475155	Strategies for the effective identification of remotely related sequences in multiple PSSM search approach
Q38942452	Strategies to reduce end-product inhibition in family 48 glycoside hydrolases
Q33280441	Strategies to search and design stabilizers of protein-protein interactions: a feasibility study
Q74449398	Strategy for membrane protein crystallization exemplified with OmpA and OmpX
Q33203190	Strategy for supplementing structure calculations using limited data with hydrophobic distance restraints
Q33662289	Strengths and weaknesses of data-driven docking in critical assessment of prediction of interactions.
Q79502773	Strong and weak hydrogen bonds in the protein-ligand interface
Q96437203	Structural Compliance - A New Metric for Protein Flexibility
Q56877735	Structural alignment and analysis of two distantly related proteins:Aplysia limacina myoglobin and sea lamprey globin
Q73540955	Structural alignment of ferredoxin and flavodoxin based on electrostatic potentials: implications for their interactions with photosystem I and ferredoxin-NADP reductase
Q30357671	Structural analysis and prediction of protein mutant stability using distance and torsion potentials: role of secondary structure and solvent accessibility.
Q83932046	Structural analysis of B. subtilis CcpA effector binding site
Q27673648	Structural analysis of CPF_2247, a novel α-amylase from Clostridium perfringens
Q83670942	Structural analysis of Escherichia coli C5 protein
Q46445101	Structural analysis of a set of proteins resulting from a bacterial genomics project.
Q27697412	Structural analysis of antiviral agents that interact with the capsid of human rhinoviruses
Q48007336	Structural analysis of disease-causing mutations in the P-subfamily of forkhead transcription factors
Q27652350	Structural analysis of fish versus mammalian hemoglobins: Effect of the heme pocket environment on autooxidation and hemin loss
Q60633209	Structural analysis of interactions for complex formation between Ferredoxin-NADP+ reductase and its protein partners
Q40682149	Structural analysis of nested neutralizing and non-neutralizing B cell epitopes on ricin toxin's enzymatic subunit.
Q51066564	Structural analysis of oligomeric and protofibrillar Aβ amyloid pair structures considering F20L mutation effects using molecular dynamics simulations
Q37361318	Structural analysis of protein dynamics by MD simulations and NMR spin-relaxation
Q47299327	Structural analysis of protein tyrosine phosphatase 1B reveals potentially druggable allosteric binding sites
Q43408067	Structural analysis of purified beta-adrenergic receptors
Q30196156	Structural analysis of the 2.8 A model of Xylose isomerase from Actinoplanes missouriensis
Q98830086	Structural analysis of the N-acetyltransferase Eis1 from Mycobacterium abscessus reveals the molecular determinants of its incapacity to modify aminoglycosides
Q46157805	Structural analysis of the N-terminal fragment of the antiangiogenic protein endostatin: a molecular dynamics study.
Q27703785	Structural analysis of the active site architecture of the VapC toxin from Shigella flexneri
Q27700095	Structural analysis of the polo-box domain of human Polo-like kinase 2
Q63387718	Structural analysis of the transcriptional regulator homolog protein from Pyrococcus horikoshii OT3
Q27730436	Structural analysis of the zinc hydroxide-Thr-199-Glu-106 hydrogen-bond network in human carbonic anhydrase II
Q27730209	Structural analysis of two crystal forms of lentil lectin at 1.8 A resolution
Q43956364	Structural analysis, identification, and design of calcium-binding sites in proteins
Q38330176	Structural and binding studies of the C-terminal domains of yeast TFIIF subunits Tfg1 and Tfg2.
Q35344420	Structural and biochemical analysis of mammalian methionine sulfoxide reductase B2
Q61716783	Structural and biochemical characterization of Plasmodium falciparum Hsp70-x reveals functional versatility of its C-terminal EEVN motif
Q80353260	Structural and biochemical characterization of inhibitor-1alpha
Q27679275	Structural and biochemical characterization of native and recombinant single insulin‐like growth factor‐binding domain protein (SIBD‐1) from the Central American Hunting Spider Cupiennius salei (Ctenidae)
Q27704294	Structural and biochemical insights into 7β-hydroxysteroid dehydrogenase stereoselectivity
Q42968658	Structural and catalytic roles of amino acid residues located at substrate-binding pocket in Fibrobacter succinogenes 1,3-1,4-beta-D-glucanase
Q74452358	Structural and chemical complementarity between antibodies and the crystal surfaces they recognize
Q43026411	Structural and dynamic aspects of beta-glycosidase from mesophilic and thermophilic bacteria by multitryptophanyl emission decay studies
Q30952600	Structural and dynamic effects of alpha-helix deletion in Sso7d: implications for protein thermal stability
Q33913886	Structural and dynamic effects of cholesterol at preferred sites of interaction with rhodopsin identified from microsecond length molecular dynamics simulations
Q80135996	Structural and dynamical properties of manganese catalase and the synthetic protein DF1 and their implication for reactivity from classical molecular dynamics calculations
Q38337399	Structural and energetic characterization of nucleic acid-binding to the fingers domain of Moloney murine leukemia virus reverse transcriptase.
Q45905896	Structural and energetic differences between insertions and substitutions in staphylococcal nuclease.
Q27648043	Structural and enzymatic characterization of DR1281: A calcineurin-like phosphoesterase from Deinococcus radiodurans
Q27650070	Structural and enzymatic characterization of HP0496, a YbgC thioesterase from Helicobacter pylori
Q27684204	Structural and functional analyses of catalytic domain of GH10 xylanase from Thermoanaerobacterium saccharolyticum JW/SL-YS485
Q27694654	Structural and functional analyses of human tryptophan 2,3-dioxygenase
Q27701580	Structural and functional analysis of SleL, a peptidoglycan lysin involved in germination of Bacillus spores
Q27653172	Structural and functional analysis of a novel hormone-sensitive lipase from a metagenome library
Q27666114	Structural and functional analysis of substrate recognition by the 250s loop in amylomaltase from Thermus brockianus
Q27666542	Structural and functional analysis of the Lmo2642 cyclic nucleotide phosphodiesterase from Listeria monocytogenes
Q30351948	Structural and functional characterization of BaiA, an enzyme involved in secondary bile acid synthesis in human gut microbe
Q27662216	Structural and functional characterization of CcmG from Pseudomonas aeruginosa, a key component of the bacterial cytochrome c maturation apparatus
Q91945321	Structural and functional characterization of Solanum tuberosum VDAC36
Q45017282	Structural and functional characterization of a 5,10-methenyltetrahydrofolate synthetase from Mycoplasma pneumoniae (GI: 13508087).
Q27650421	Structural and functional characterization of a novel phosphatase from the Arabidopsis thaliana gene locus At1g05000
Q27687097	Structural and functional characterization of a novel α/β hydrolase from cariogenic pathogen Streptococcus mutans
Q27658892	Structural and functional characterization of a promiscuous feruloyl esterase (Est1E) from the rumen bacterium Butyrivibrio proteoclasticus
Q52678573	Structural and functional characterization of binding sites in metallocarboxypeptidases based on Optimal Docking Area analysis
Q27677483	Structural and functional characterization of solute binding proteins for aromatic compounds derived from lignin:p-Coumaric acid and related aromatic acids
Q90606858	Structural and functional characterization of type three secretion system ATPase PscN and its regulator PscL from Pseudomonas aeruginosa
Q27621692	Structural and functional differences of two toxins from the scorpion Pandinus imperator
Q58881508	Structural and functional effects of disease-causing amino acid substitutions affecting residues Ala72 and Glu76 of the protein tyrosine phosphatase SHP-2
Q54463124	Structural and functional evolution of transthyretin and transthyretin-like proteins
Q74015801	Structural and functional properties of a Bacillus subtilis temperature-sensitive sigma(A) factor
Q33956462	Structural and functional properties of hemocyanin from Cyanagraea praedator, a deep‐sea hydrothermal vent crab
Q44649576	Structural and functional relations among thioredoxins of different species
Q27682252	Structural and functional studies of atrans-acyltransferase polyketide assembly line enzyme that catalyzes stereoselective α- and β-ketoreduction
Q27657257	Structural and functional studies of the potent anti-HIV chemokine variant P2-RANTES
Q27644411	Structural and kinetic analysis of proton shuttle residues in the active site of human carbonic anhydrase III
Q27685369	Structural and mutational analyses of Aes, an inhibitor of MalT in Escherichia coli
Q27694789	Structural and mutational analysis of a monomeric and dimeric form of a single domain antibody with implications for protein misfolding
Q47430906	Structural and sequence comparisons arising from the solution structure of the transcription elongation factor NusG from Thermus thermophilus
Q43498896	Structural and sequence features of two residue turns in beta-hairpins
Q46931828	Structural and thermodynamic consequences of removal of a conserved disulfide bond from equine beta-lactoglobulin
Q34348491	Structural and thermodynamic folding characterization of triosephosphate isomerases from Trichomonas vaginalis reveals the role of destabilizing mutations following gene duplication
Q27667226	Structural architecture of Galdieria sulphuraria DCN1L
Q71774371	Structural aspects of the functional modules in human protein kinase-C alpha deduced from comparative analyses
Q54438227	Structural assessment of glycyl mutations in invariantly conserved motifs
Q91778762	Structural basis for -35 element recognition by σ4 chimera proteins and their interactions with PmrA response regulator
Q31011437	Structural basis for SUMO-E2 interaction revealed by a complex model using docking approach in combination with NMR data
Q34802689	Structural basis for a ribofuranosyl binding protein: Insights into the furanose specific transport
Q27630848	Structural basis for altered activity of M- and H-isozyme forms of human lactate dehydrogenase
Q47672472	Structural basis for binding and transfer of heme in bacterial heme-acquisition systems
Q27666047	Structural basis for branching-enzyme activity of glycoside hydrolase family 57: structure and stability studies of a novel branching enzyme from the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1
Q27704007	Structural basis for cellulose binding by the type A carbohydrate-binding module 64 of Spirochaeta thermophila
Q27658970	Structural basis for regulation of poly-SUMO chain by a SUMO-like domain of Nip45
Q45080412	Structural basis for serpin inhibitor activity
Q64038856	Structural basis for specificity of papain-like cysteine protease proregions toward their cognate enzymes
Q27652193	Structural basis for sugar recognition, including the Tn carcinoma antigen, by the lectin SNA-II from Sambucus nigra
Q27618299	Structural basis for the activity of two muconate cycloisomerase variants toward substituted muconates
Q43608570	Structural basis for the appearance of a molten globule state in chimeric molecules derived from lysozyme and alpha-lactalbumin
Q27649508	Structural basis for the cold adaptation of psychrophilic M37 lipase from Photobacterium lipolyticum
Q46251109	Structural basis for the complete loss of GSK3beta catalytic activity due to R96 mutation investigated by molecular dynamics study
Q80278836	Structural basis for the observed differential magnetic anisotropic tensorial values in calcium binding proteins
Q27684756	Structural basis for the β-lactamase activity of EstU1, a family VIII carboxylesterase
Q43024589	Structural basis for thermostability and identification of potential active site residues for adenylate kinases from the archaeal genus Methanococcus.
Q46103514	Structural basis for type I and type II deficiencies of antithrombotic plasma protein C: patterns revealed by three-dimensional molecular modelling of mutations of the protease domain
Q27643631	Structural basis of allele variation of human thiopurine-S-methyltransferase
Q55072903	Structural basis of conformational variance in phosphorylated and non-phosphorylated states of PKCβII.
Q51656662	Structural basis of hierarchical multiple substates of a protein. I: Introduction
Q51656679	Structural basis of hierarchical multiple substates of a protein. II: Monte Carlo simulation of native thermal fluctuations and energy minimization
Q51656674	Structural basis of hierarchical multiple substates of a protein. III: Side chain and main chain local conformations
Q45102853	Structural basis of hierarchical multiple substates of a protein. IV: Rearrangements in atom packing and local deformations
Q51656666	Structural basis of hierarchical multiple substates of a protein. V: Nonlocal deformations
Q27766340	Structural basis of increased resistance to thermal denaturation induced by single amino acid substitution in the sequence of beta-glucosidase A from Bacillus polymyxa
Q104503361	Structural basis of mutants of PET-degrading enzyme from Saccharomonospora viridis AHK190 with high activity and thermal stability
Q27649291	Structural basis of octanoic acid recognition by lipoate-protein ligase B
Q42828980	Structural basis of oncogenic activation caused by point mutations in the kinase domain of the MET proto-oncogene: modeling studies
Q27728173	Structural basis of reversine selectivity in inhibiting Mps1 more potently than aurora B kinase
Q27621085	Structural basis of the catalytic role of Glu301 in Anabaena PCC 7119 ferredoxin-NADP+ reductase revealed by x-ray crystallography
Q60633217	Structural basis of the catalytic role of Glu301 inAnabaena PCC 7119 ferredoxin-NADP+ reductase revealed by x-ray crystallography
Q43024866	Structural basis of the properties of an industrially relevant thermophilic xylanase
Q43018634	Structural basis of the substrate subsite and the highly thermal stability of xylanase 10B from Thermotoga maritima MSB8.
Q27656652	Structural basis of typhoid: Salmonella typhi type IVb pilin (PilS) and cystic fibrosis transmembrane conductance regulator interaction
Q46971343	Structural bioinformatics analysis of enzymes involved in the biosynthesis pathway of the hypermodified nucleoside ms(2)io(6)A37 in tRNA.
Q47902093	Structural bioinformatics mutation analysis reveals genotype-phenotype correlations in von Hippel-Lindau disease and suggests molecular mechanisms of tumorigenesis
Q27737057	Structural change and receptor binding in a chemokine mutant with a rearranged disulfide: X-ray structure of E38C/C50AIL-8 at 2 A resolution
Q83530742	Structural changes of Listeria monocytogenes sortase A: A key to understanding the catalytic mechanism
Q53323738	Structural characterization by nuclear magnetic resonance of the impact of phosphorylation in the proline-rich region of the disordered Tau protein
Q36060114	Structural characterization of AtmS13, a putative sugar aminotransferase involved in indolocarbazole AT2433 aminopentose biosynthesis
Q27650879	Structural characterization of CalO2: A putative orsellinic acid P450 oxidase in the calicheamicin biosynthetic pathway
Q33240038	Structural characterization of Salmonella typhimurium YeaZ, an M22 O-sialoglycoprotein endopeptidase homolog
Q27688004	Structural characterization of a ligand-bound form of Bacillus subtilis FadR involved in the regulation of fatty acid degradation
Q30587173	Structural characterization of a methionine-rich, emulsifying protein from sunflower seed
Q27689012	Structural characterization of a new N-substituted pantothenamide bound to pantothenate kinases from Klebsiella pneumoniae and Staphylococcus aureus
Q46032479	Structural characterization of an iron-sulfur cluster assembly protein IscU in a zinc-bound form.
Q27674550	Structural characterization of human Uch37
Q36789994	Structural characterization of proteins using residue environments
Q79805169	Structural characterization of the Acetobacter xylinum endo-beta-1,4-glucanase CMCax required for cellulose biosynthesis
Q48268242	Structural characterization of the PTS IIA and IIB proteins associated with pneumococcal fucose utilization.
Q81979774	Structural characterization of the alpha-hemolysin monomer from Staphylococcus aureus
Q33270037	Structural characterization of the functional regions in the archaeal protein Sso7d
Q48209789	Structural characterization of the heme-based oxygen sensor, AfGcHK, its interactions with the cognate response regulator, and their combined mechanism of action in a bacterial two-component signaling system.
Q27667659	Structural characterization of the mitomycin 7-O-methyltransferase
Q58111155	Structural characterization of the neurabin sterile alpha motif domain
Q46251092	Structural characterization of the tunnels of Mycobacterium tuberculosis truncated hemoglobin N from molecular dynamics simulations
Q37289657	Structural characterization of the zinc binding domain in cytosolic PSD-95 interactor (cypin): Role of zinc binding in guanine deamination and dendrite branching
Q34019423	Structural characterization of two pore-forming peptides: consequences of introducing a C-terminal tryptophan
Q73393627	Structural characterization of two tandemly arranged DNA methyltransferase genes from Neisseria gonorrhoeae MS11: N4-cytosine specific M.NgoMXV and nonfunctional 5-cytosine-type M.NgoMorf2P
Q93012387	Structural characterization of β-ketoacyl ACP synthase I bound to platencin and fragment screening molecules at two substrate binding sites
Q46431511	Structural classification of CDR-H3 revisited: a lesson in antibody modeling
Q52247913	Structural classification of alphabetabeta and betabetaalpha supersecondary structure units in proteins
Q30344339	Structural classification of thioredoxin-like fold proteins.
Q30390364	Structural comparison and classification of alpha-helical transmembrane domains based on helix interaction patterns
Q27654074	Structural comparison of chromosomal and exogenous dihydrofolate reductase from Staphylococcus aureus in complex with the potent inhibitor trimethoprim
Q79212130	Structural comparison of oxidized and reduced FKBP13 from Arabidopsis thaliana
Q54756788	Structural comparison of the prokaryotic ribosomal proteins L7/L12 and L30.
Q91142497	Structural complementarity of distance constraints obtained from chemical cross-linking and amino acid coevolution
Q80389889	Structural components of SCAN-domain dimerizations
Q46140155	Structural consensus in ligand-protein docking identifies recognition peptide motifs that bind streptavidin
Q73062305	Structural consequences of an amino acid deletion in the B1 domain of protein G
Q27681708	Structural conservation of the B subunit in the ammonia monooxygenase/particulate methane monooxygenase superfamily
Q27651627	Structural coupling between FKBP12 and buried water
Q27739356	Structural definition of the C5a C terminus by two-dimensional nuclear magnetic resonance spectroscopy
Q27704385	Structural determinants in bacterial 2-keto-3-deoxy-D-gluconate dehydrogenase KduD for dual-coenzyme specificity
Q77360649	Structural determinants of binding and specificity in transforming growth factor–receptor interactions
Q56877631	Structural determinants of ligand migration in Mycobacterium tuberculosis truncated hemoglobin O
Q37436023	Structural determinants of species-selective substrate recognition in human and Drosophila serotonin transporters revealed through computational docking studies
Q47643263	Structural determinants of the conformations of medium-sized loops in proteins
Q79883952	Structural determinants responsible for the thermostability of Sso7d and its single point mutants
Q57070597	Structural determination of archaeal UDP-N-acetylglucosamine 4-epimerase from Methanobrevibacter ruminantium M1 in complex with the bacterial cell wall intermediate UDP-N-acetylmuramic acid
Q87461806	Structural differences among subfamilies of EF-hand proteins--a view from the pseudo two-fold symmetry axis
Q57355701	Structural differences between allelic variants of the ovine prion protein revealed by molecular dynamics simulations
Q92926953	Structural differences between the ectodomains of murine and human CD98hc
Q34713870	Structural disorder serves as a weak signal for intracellular protein degradation.
Q34680376	Structural divergence is more extensive than sequence divergence for a family of intrinsically disordered proteins
Q30429975	Structural diversity of sequentially identical subsequences of proteins: Identical octapeptides can have different conformations
Q30487951	Structural diversity of the epigenetics pocketome.
Q33500238	Structural domain-domain interactions: assessment and comparison with protein-protein interaction data to improve the interactome
Q35824282	Structural dynamics of an ionotropic glutamate receptor
Q47608094	Structural dynamics of nucleosome core particle: comparison with nucleosomes containing histone variants.
Q96437228	Structural dynamics of pentapeptide repeat proteins
Q28264619	Structural dynamics of the mitochondrial ADP/ATP carrier revealed by molecular dynamics simulation studies
Q34254774	Structural dynamics of the monoamine transporter homolog LeuT from accelerated conformational sampling and channel analysis
Q27642125	Structural effects induced by mutagenesis affected by crystal packing factors: the structure of a 30-51 disulfide mutant of basic pancreatic trypsin inhibitor
Q92952309	Structural effects of divalent calcium cations on the α7 nicotinic acetylcholine receptor: A molecular dynamics simulation study
Q88142869	Structural effects of point mutations in proteins
Q27652649	Structural elucidation of the Cys-His-Glu-Asn proteolytic relay in the secreted CHAP domain enzyme from the human pathogenStaphylococcus saprophyticus
Q57206223	Structural energetics of peptide recognition: Angiotensin II/antibody binding
Q40825795	Structural energetics of the molten globule state
Q27689006	Structural evidence for a constrained conformation of short CDR-L3 in antibodies
Q42624873	Structural evidence for a functionally relevant second camphor binding site in P450cam: model for substrate entry into a P450 active site
Q27625388	Structural evidence for recognition of a single epitope by two distinct antibodies
Q56984915	Structural evidence for variable oligomerization of the N-terminal domain of cyclase-associated protein (CAP)
Q27673668	Structural evidence that puromycin hydrolase is a new type of aminopeptidase with a prolyl oligopeptidase family fold
Q48342777	Structural facets of disease-linked human prion protein mutants: a molecular dynamic study
Q30155210	Structural features of cholesteryl ester transfer protein: a molecular dynamics simulation study
Q42648833	Structural features of ribonucleotide reductase
Q27657493	Structural features of the Nostoc punctiforme debranching enzyme reveal the basis of its mechanism and substrate specificity
Q34330580	Structural features of the inactive and active states of the melanin-concentrating hormone receptors: insights from molecular simulations.
Q32035348	Structural features of the plasmid pMV158-encoded transcriptional repressor CopG, a protein sharing similarities with both helix-turn-helix and beta-sheet DNA binding proteins
Q62019583	Structural features of the plasmid pMV158-encoded transcriptional repressor CopG, a protein sharing similarities with both helix-turn-helix and β-sheet DNA binding proteins
Q30412983	Structural features that predict real-value fluctuations of globular proteins
Q100388562	Structural fluctuations and mechanical stabilities of the metamorphic protein RfaH
Q52938509	Structural genomics analysis: characteristics of atypical, common, and horizontally transferred folds
Q27700949	Structural genomics for drug design against the pathogen Coxiella burnetii
Q27640991	Structural genomics of Caenorhabditis elegans: Triosephosphate isomerase
Q47307280	Structural genomics of Caenorhabditis elegans: crystal structure of the tropomodulin C-terminal domain
Q27642613	Structural genomics of Caenorhabditis elegans: structure of dihydropteridine reductase
Q47608931	Structural genomics of Pyrococcus furiosus: X-ray crystallography reveals 3D domain swapping in rubrerythrin
Q27642614	Structural genomics of caenorhabditis elegans: crystal structure of calmodulin
Q27653638	Structural genomics reveals EVE as a new ASCH/PUA-related domain
Q43544497	Structural homology among the peroxidase enzyme family revealed by hydrophobic cluster analysis
Q36847090	Structural homology of spinach acyl carrier protein and Escherichia coli acyl carrier protein based on NMR data
Q27631613	Structural implications of drug-resistant mutants of HIV-1 protease: high-resolution crystal structures of the mutant protease/substrate analogue complexes
Q43014937	Structural insight for the roles of fas death domain binding to fadd and oligomerization degree of the fas–fadd complex in the death‐inducing signaling complex formation: A computational study
Q27675491	Structural insight into mechanism and diverse substrate selection strategy of L-ribulokinase
Q45223476	Structural insight into the UNC-45-myosin complex
Q53551591	Structural insight into the distinct properties of copper transport by the Helicobacter pylori CopP protein
Q27679287	Structural insight into the evolution of a new chemokine family from zebrafish
Q27647662	Structural insight of the role of the Hahella chejuensis HapK protein in prodigiosin biosynthesis
Q27681484	Structural insights into FRS2α PTB domain recognition by neurotrophin receptor TrkB
Q27657490	Structural insights into Staphylococcus aureus enoyl-ACP reductase (FabI), in complex with NADP and triclosan
Q83349776	Structural insights into a low‐spin myoglobin variant with bis‐histidine coordination from molecular modeling
Q27679522	Structural insights into catalysis by βC-S lyase from Streptococcus anginosus
Q39000675	Structural insights into human microsomal epoxide hydrolase by combined homology modeling, molecular dynamics simulations, and molecular docking calculations
Q27667433	Structural insights into piRNA recognition by the human PIWI-like 1 PAZ domain
Q42592414	Structural insights into recognition of beta2-glycoprotein I by the lipoprotein receptors.
Q27690230	Structural insights into substrate and coenzyme preference by SDR family protein Gox2253 from Gluconobater oxydans
Q54451013	Structural insights into the GTPase domain of Escherichia coli MnmE protein.
Q27687643	Structural insights into the aggregation behavior of Murraya koenigii miraculin-like protein below pH 7.5
Q46668381	Structural insights into the cellular retinaldehyde-binding protein (CRALBP).
Q84171315	Structural insights into the metal binding properties of hypothetical protein MJ0754 from Methanococcus jannaschii
Q27690813	Structural insights into the stabilization of active, tetrameric DszC by its C-terminus
Q35875958	Structural integrity of the ribonuclease H domain in HIV-1 reverse transcriptase.
Q43032019	Structural investigation into the C-terminal extension of the ene-reductase from Ralstonia (Cupriavidus) metallidurans.
Q47974611	Structural investigation of C4b-binding protein by molecular modeling: localization of putative binding sites.
Q42554450	Structural investigation of the complexation properties between horse spleen apoferritin and metalloporphyrins
Q27660211	Structural investigation of transcriptional regulator HlyIIR: influence of a disordered region on protein fold and dimerization
Q73134452	Structural mapping of single cysteine mutants of cardiac troponin I
Q30371571	Structural mapping of the coiled-coil domain of a bacterial condensin and comparative analyses across all domains of life suggest conserved features of SMC proteins.
Q42716640	Structural mechanism associated with domain opening in gain-of-function mutations in SHP2 phosphatase.
Q39864197	Structural mechanisms of constitutive activation in the C5a receptors with mutations in the extracellular loops: Molecular modeling study
Q51009394	Structural memory of natively unfolded tau protein detected by small-angle X-ray scattering
Q77603403	Structural model for family 32 of glycosyl-hydrolase enzymes
Q47974642	Structural model of Dex protein from Penicillium minioluteum and its implications in the mechanism of catalysis
Q45250396	Structural model of human GAD65: prediction and interpretation of biochemical and immunogenic features
Q52297894	Structural model of the anti-snake-toxin antibody, M alpha 2,3.
Q71537025	Structural model of the photosynthetic reaction center of Rhodobacter capsulatus
Q54631335	Structural modeling and electrostatic properties of aspartate transcarbamylase from Saccharomyces cerevisiae.
Q84071510	Structural modeling and molecular dynamics simulation of the actin filament
Q33180899	Structural modeling of a plant disease resistance gene product domain
Q28218002	Structural modeling of ataxin-3 reveals distant homology to adaptins
Q91793310	Structural modeling of protein complexes: Current capabilities and challenges
Q74363289	Structural modeling of the complex between an acetylcholine receptor-mimicking antibody and its snake toxin antigen
Q52229470	Structural models of the bovine papillomavirus E5 protein
Q53614710	Structural models of the snake venom factor V activators from Daboia russelli and Daboia lebetina
Q48177488	Structural motifs in which β-strands are clipped together with the П-like module.
Q30391301	Structural mutation analysis of PTEN and its genotype-phenotype correlations in endometriosis and cancer
Q27664066	Structural origins of pH-dependent chemical shifts in the B1 domain of protein G
Q44125121	Structural parameterization of the binding enthalpy of small ligands
Q33449219	Structural plasticity of staphylococcal nuclease probed by perturbation with pressure and pH.
Q43031949	Structural plasticity of thermophilic serine hydroxymethyltransferases
Q47258381	Structural polymorphism of a marginally stable 4-alpha-helical bundle. Images of a trapped molten globule?
Q46564490	Structural prediction of peptides binding to MHC class I molecules
Q58035264	Structural prediction of the β-domain of metallothionein-3 by molecular dynamics simulation
Q28156101	Structural principles for the propeller assembly of beta-sheets: the preference for seven-fold symmetry
Q28142324	Structural principles governing domain motions in proteins
Q29305034	Structural principles governing domain motions in proteins
Q28270770	Structural principles of alpha/beta barrel proteins: the packing of the interior of the sheet
Q28241151	Structural principles of leucine-rich repeat (LRR) proteins
Q48046294	Structural properties of amyloid β(1-40) dimer explored by replica exchange molecular dynamics simulations.
Q42030679	Structural properties of the DNA-bound form of a novel tandem repeat DNA-binding domain, STPR.
Q45396888	Structural properties of the human respiratory syncytial virus P protein: evidence for an elongated homotetrameric molecule that is the smallest orthologue within the family of paramyxovirus polymerase cofactors
Q49701383	Structural quality of unrefined models in protein docking
Q27660059	Structural rationale for the short branched substrate specificity of the glycogen debranching enzyme GlgX
Q46934310	Structural rationalization of novel drug metabolizing mutants of cytochrome P450 BM3.
Q40295014	Structural refinement of protein segments containing secondary structure elements: Local sampling, knowledge-based potentials, and clustering
Q42426874	Structural refinement of the hERG1 pore and voltage-sensing domains with ROSETTA-membrane and molecular dynamics simulations.
Q30421557	Structural relationships of homologous proteins as a fundamental principle in homology modeling
Q47581961	Structural repertoire of immunoglobulin λ light chains
Q42275220	Structural requirements for enzymatic activities of foamy virus protease-reverse transcriptase
Q36381221	Structural review of PPARγ in complex with ligands: Cartesian- and dihedral angle principal component analyses of X-ray crystallographic data.
Q48342123	Structural role of a conserved active site cis proline in the Thermotoga maritima acetyl esterase from the carbohydrate esterase family 7.
Q30327292	Structural stability of binding sites: consequences for binding affinity and allosteric effects.
Q71705245	Structural stability of disulfide mutants of basic pancreatic trypsin inhibitor: a molecular dynamics study
Q27621075	Structural studies of FIV and HIV-1 proteases complexed with an efficient inhibitor of FIV protease
Q35751293	Structural studies of a signal peptide in complex with signal peptidase I cytoplasmic domain: the stabilizing effect of membrane-mimetics on the acquired fold
Q36707190	Structural studies of a synthetic peptide derived from the carboxyl-terminal domain of RNA polymerase II.
Q27690084	Structural studies of bovine, equine, and leporine serum albumin complexes with naproxen
Q27663100	Structural studies of mutant forms of the PQQ-forming enzyme PqqC in the presence of product and substrate
Q46668183	Structural studies of prephenate dehydratase from Mycobacterium tuberculosis H37Rv by SAXS, ultracentrifugation, and computational analysis.
Q46764636	Structural studies of shikimate 5-dehydrogenase from Mycobacterium tuberculosis
Q27666243	Structural studies of the Nudix GDP-mannose hydrolase from E. coli reveals a new motif for mannose recognition
Q27642090	Structural studies of the retroviral proteinase from avian myeloblastosis associated virus
Q27684462	Structural studies of the tethered N-terminus of the Alzheimer's disease amyloid-β peptide
Q90388690	Structural studies on 10-hydroxygeraniol dehydrogenase: A novel linear substrate-specific dehydrogenase from Catharanthus roseus
Q27640401	Structural studies on MtRecA-nucleotide complexes: insights into DNA and nucleotide binding and the structural signature of NTP recognition
Q27657590	Structural studies on cytosolic domain of magnesium transporter MgtE fromEnterococcus faecalis
Q27664980	Structural studies on the enzyme complex isopropylmalate isomerase (LeuCD) from Mycobacterium tuberculosis
Q45959208	Structural study of Carcinus maenas hemocyanin by native ESI-MS: interaction with L-lactate and divalent cations.
Q34062344	Structural superposition of proteins with unknown alignment and detection of topological similarity using a six-dimensional search algorithm
Q35501780	Structural templates for comparative protein docking
Q56927698	Structural thermal adaptation of β-tubulins from the Antarctic psychrophilic protozoan Euplotes focardii
Q73025527	Structural thermodynamics of a random coil protein in guanidine hydrochloride
Q46580532	Structural thermodynamics of protein preferential solvation: osmolyte solvation of proteins, aminoacids, and peptides
Q35948983	Structural transitions and oligomerization along polyalanine fibril formation pathways from computer simulations
Q30427554	Structural trees for protein superfamilies
Q27656655	Structural understanding of stabilization patterns in engineered bispecific Ig-like antibody molecules
Q57707009	Structural variation and immune recognition of the P1.2 subtype meningococcal antigen
Q59226365	Structural variation manipulates the differential oxidative susceptibility and conformational stability of apolipoprotein E isoforms
Q30155162	Structural, energetic, and dynamic responses of the native state ensemble of staphylococcal nuclease to cavity-creating mutations.
Q27664737	Structural, functional, and bioinformatics studies reveal a new snake venom homologue phospholipase A₂ class
Q30152895	Structure alignment of membrane proteins: Accuracy of available tools and a consensus strategy
Q51575991	Structure alignment of membrane proteins: Accuracy of available tools and a consensus strategy.
Q30350634	Structure alignment via Delaunay tetrahedralization.
Q38513454	Structure analysis of peptide deformylase from Bacillus cereus
Q28592797	Structure and DNA binding characteristics of the three-Cys(2)His(2) domain of mouse testis zinc finger protein
Q27666116	Structure and DNA‐binding activity of the Pyrococcus furiosus SMC protein hinge domain
Q27683578	Structure and activity of the NAD(P)+-dependent succinate semialdehyde dehydrogenase YneI from Salmonella typhimurium
Q27649055	Structure and biochemical analysis of Kokobera virus helicase
Q45062754	Structure and catalytic activation of the TRIM23 RING E3 ubiquitin ligase
Q27637709	Structure and cooperativity of a T-state mutant of histidine decarboxylase from Lactobacillus 30a
Q30176016	Structure and dynamic properties of the single disulfide-deficient alpha-amylase inhibitor [C45A/C73A]tendamistat: an NMR study
Q93059679	Structure and dynamics at N- and C-terminal regions of intrinsically disordered human c-Myc PEST degron reveal a pH-induced transition
Q30009287	Structure and dynamics of DRD4 bound to an agonist and an antagonist using in silico approaches
Q27646758	Structure and dynamics of gamma-SNAP: insight into flexibility of proteins from the SNAP family
Q30427174	Structure and dynamics of the M13 coat signal sequence in membranes by multidimensional high-resolution and solid-state NMR spectroscopy
Q111291711	Structure and dynamics of the SARS‐CoV ‐2 envelope protein monomer
Q34372533	Structure and dynamics of the human pleckstrin DEP domain: distinct molecular features of a novel DEP domain subfamily
Q72416543	Structure and dynamics of the neutrophil defensins NP-2, NP-5, and HNP-1: NMR studies of amide hydrogen exchange kinetics
Q30588345	Structure and dynamics of the pore-lining helix of the nicotinic receptor: MD simulations in water, lipid bilayers, and transbilayer bundles
Q27640399	Structure and dynamics of the potato carboxypeptidase inhibitor by 1H and 15N NMR
Q54756726	Structure and energetics of ligand binding to proteins: Escherichia coli dihydrofolate reductase-trimethoprim, a drug-receptor system.
Q46565537	Structure and energy landscape of a photoswitchable peptide: a replica exchange molecular dynamics study
Q43967675	Structure and enzymatic properties of a chimeric bacteriophage RB69 DNA polymerase and single-stranded DNA binding protein with increased processivity
Q34768272	Structure and folding of disulfide-rich miniproteins: insights from molecular dynamics simulations and MM-PBSA free energy calculations
Q90300132	Structure and function insights garnered from in silico modeling of the thrombospondin type-1 domain-containing 7A antigen
Q27683997	Structure and function of a TetR family transcriptional regulator, SbtR, from thermus thermophilus HB8
Q27683810	Structure and function of an acetyl xylan esterase (Est2A) from the rumen bacterium Butyrivibrio proteoclasticus
Q74449405	Structure and function of chromophores in R-Phycoerythrin at 1.9 A resolution
Q27684460	Structure and function ofEscherichia coliRimK, an ATP-grasp fold,l-glutamyl ligase enzyme
Q27702575	Structure and functional analysis of the siderophore periplasmic binding protein from the fuscachelin gene cluster of Thermobifida fusca
Q36586233	Structure and functional characterization of a bile acid 7α dehydratase BaiE in secondary bile acid synthesis
Q27663110	Structure and interactions of the C-terminal metal binding domain of Archaeoglobus fulgidus CopA
Q36788618	Structure and internal dynamics of the bovine pancreatic trypsin inhibitor in aqueous solution from long-time molecular dynamics simulations.
Q46804016	Structure and mechanism of the farnesyl diphosphate synthase from Trypanosoma cruzi: implications for drug design
Q27661461	Structure and oligomerization of the PilC type IV pilus biogenesis protein from Thermus thermophilus
Q54203727	Structure and properties of AB21, a novel Agaricus bisporus protein with structural relation to bacterial pore-forming toxins
Q27643329	Structure and properties of a truely apo form of AraC dimerization domain
Q27646760	Structure and quantum chemical analysis of NAD+-dependent isocitrate dehydrogenase: hydride transfer and co-factor specificity
Q34735386	Structure and specificity of FEN-1 from Methanopyrus kandleri
Q27689552	Structure and specificity of an antibody targeting a proteolytically cleaved IgG hinge
Q51370409	Structure and stability of a model three-helix-bundle protein on tailored surfaces
Q69658326	Structure and thermal stability of monomeric bacteriorhodopsin in mixed phospholipid/detergent micelles
Q42181496	Structure based computational assessment of channel properties of assembled ORF-8a from SARS-CoV.
Q43445023	Structure based mechanism of the Ca(2+)-induced release of coelenterazine from the Renilla binding protein
Q42612067	Structure classification-based assessment of CASP3 predictions for the fold recognition targets
Q42643528	Structure conservation in cytochromes P450.
Q52309185	Structure conservation in lipoxygenases: structural analysis of soybean lipoxygenase-1 and modeling of human lipoxygenases
Q27683745	Structure determination and refinement of Bacillus stearothermophilus lactate dehydrogenase
Q27650209	Structure determination of Discoidin II from Dictyostelium discoideum and carbohydrate binding properties of the lectin domain
Q31056365	Structure determination of a new protein from backbone-centered NMR data and NMR-assisted structure prediction
Q51610756	Structure determination of a protein assembly by amino acid selective cross-saturation
Q27732038	Structure determination of feline panleukopenia virus empty particles
Q34555581	Structure determination of symmetric homo-oligomers by a complete search of symmetry configuration space, using NMR restraints and van der Waals packing.
Q57208986	Structure is three to ten times more conserved than sequence-A study of structural response in protein cores
Q52300233	Structure model of a complex between the factor for inversion stimulation (FIS) and DNA: modeling protein-DNA complexes with dyad symmetry and known protein structures
Q57752571	Structure modeling, ligand binding, and binding affinity calculation (LR-MM-PBSA) of human heparanase for inhibition and drug design
Q42614811	Structure modelling and site-directed mutagenesis of the rat aromatic L-amino acid pyridoxal 5'-phosphate-dependent decarboxylase: a functional study
Q30361168	Structure networks of E. coli glutaminyl-tRNA synthetase: effects of ligand binding.
Q27648278	Structure of 2-deoxy-scyllo-inosose synthase, a key enzyme in the biosynthesis of 2-deoxystreptamine-containing aminoglycoside antibiotics, in complex with a mechanism-based inhibitor and NAD+
Q27639584	Structure of 2C-methyl-D-erythrol-2,4-cyclodiphosphate synthase from Haemophilus influenzae: activation by conformational transition
Q27701666	Structure of Ctk3, a subunit of the RNA polymerase II CTD kinase complex, reveals a noncanonical CTD-interacting domain fold
Q60913190	Structure of HI0073 from Haemophilus influenzae, the nucleotide-binding domain of a two-protein nucleotidyl transferase
Q27639733	Structure of HI1333 (YhbY), a putative RNA-binding protein from Haemophilus influenzae
Q27651183	Structure of HP0564 from Helicobacter pylori identifies it as a new transcriptional regulator
Q43864571	Structure of Met-enkephalin in explicit aqueous solution using replica exchange molecular dynamics
Q27735387	Structure of Semliki Forest virus core protein
Q27646620	Structure of Xanthomonas axonopodis pv. citri YaeQ reveals a new compact protein fold built around a variation of the PD-(D/E)XK nuclease motif
Q46391927	Structure of YciI from Haemophilus influenzae (HI0828) reveals a ferredoxin-like alpha/beta-fold with a histidine/aspartate centered catalytic site.
Q30435859	Structure of YidB protein from Shigella flexneri shows a new fold with homeodomain motif
Q27650324	Structure of YraM, a protein essential for growth of Haemophilus influenzae
Q60238208	Structure of a carbohydrate esterase from Bacillus anthracis
Q34989735	Structure of a cupin protein Plu4264 from Photorhabdus luminescens subsp. laumondii TTO1 at 1.35 Å resolution
Q83203031	Structure of a glutathione conjugate bound to the active site of aldose reductase
Q46464605	Structure of a glycoside hydrolase family 50 enzyme from a subfamily that is enriched in human gut microbiome bacteroidetes
Q27633847	Structure of a legume lectin from the bark of Robinia pseudoacacia and its complex with N-acetylgalactosamine
Q27654990	Structure of a pullulanase from Bacillus acidopullulyticus
Q27664156	Structure of a putative BenF-like porin from Pseudomonas fluorescens Pf-5 at 2.6 Å resolution
Q67584046	Structure of a rhombohedral R6 insulin/phenol complex
Q28283187	Structure of a ribulose 5-phosphate 3-epimerase from Plasmodium falciparum
Q27733437	Structure of a ternary complex of proteinase K, mercury, and a substrate-analogue hexa-peptide at 2.2 A resolution
Q45039419	Structure of an anti-DNA fab complexed with a non-DNA ligand provides insights into cross-reactivity and molecular mimicry
Q27635358	Structure of an anti-HIV monoclonal Fab antibody fragment specific to a gp120 C-4 region peptide
Q27667514	Structure of an archaeal-type phosphoenolpyruvate carboxylase sensitive to inhibition by aspartate
Q30196213	Structure of an insect virus at 3.0 A resolution
Q43512274	Structure of an intermediate in the unfolding of creatine kinase
Q27648031	Structure of aspartate racemase complexed with a dual substrate analogue, citric acid, and implications for the reaction mechanism
Q27646975	Structure of biosynthetic N-acetylornithine aminotransferase from Salmonella typhimurium: studies on substrate specificity and inhibitor binding
Q43694842	Structure of bovine alpha-1,3-galactosyltransferase and its complexes with UDP and DPGal inferred from molecular modeling
Q50148706	Structure of catalase HPII from Escherichia coli at 1.9 A resolution
Q78675908	Structure of deoxyhemoglobin: ionizable groups and polyethylene glycol
Q27662219	Structure of full-length class I chitinase from rice revealed by X-ray crystallography and small-angle X-ray scattering
Q27659698	Structure of human CLIC3 at 2 A resolution
Q27695608	Structure of human SNX10 reveals insights into its role in human autosomal recessive osteopetrosis
Q44252303	Structure of human aldose reductase holoenzyme in complex with statil: an approach to structure-based inhibitor design of the enzyme
Q27657905	Structure of hyperthermophilic endocellulase from Pyrococcus horikoshii
Q27703982	Structure of iron saturated C-lobe of bovine lactoferrin at pH 6.8 indicates a weakening of iron coordination
Q37471218	Structure of phage protein BC1872 from Bacillus cereus, a singleton with new fold.
Q27649514	Structure of protein PH0536 from Pyrococcus horikoshii at 1.7 A resolution reveals a novel assembly of an oligonucleotide/oligosaccharide-binding fold and an alpha-helical bundle
Q27634879	Structure of rat parvalbumin with deleted AB domain: implications for the evolution of EF hand calcium-binding proteins and possible physiological relevance
Q45233913	Structure of ricin A-chain at 2.5 A.
Q30372288	Structure of ricin B-chain at 2.5 A resolution.
Q27743059	Structure of soybean lipoxygenase L3 and a comparison with its L1 isoenzyme
Q27663523	Structure of the ATP-binding domain of Plasmodium falciparum Hsp90
Q27667121	Structure of the C-terminal domain of Saccharomyces cerevisiae Nup133, a component of the nuclear pore complex
Q27640400	Structure of the Clade 1 catalase, CatF of Pseudomonas syringae, at 1.8 A resolution
Q27667228	Structure of the C‐terminal heme‐binding domain of THAP domain containing protein 4 from Homo sapiens
Q27675629	Structure of the DNA-bound T-box domain of human TBX1, a transcription factor associated with the DiGeorge syndrome
Q27648881	Structure of the Drosophila nucleosome core particle highlights evolutionary constraints on the H2A-H2B histone dimer
Q27657487	Structure of the EMMPRIN N-terminal domain 1: dimerization via beta-strand swapping
Q44125849	Structure of the LAV6 peptide: A nucleation site for the correct receptor-induced refolding of the CD4-binding domain of HIV1 gp 120
Q27666113	Structure of the Mycobacterium tuberculosis OmpATb protein: a model of an oligomeric channel in the mycobacterial cell wall
Q27676879	Structure of the NLRP1 caspase recruitment domain suggests potential mechanisms for its association with procaspase-1
Q27652351	Structure of the OSR1 kinase, a hypertension drug target
Q27677252	Structure of the RNA-directed RNA Polymerase from the cystovirus ϕ12
Q27652871	Structure of the S1S2 glutamate binding domain of GLuR3
Q27644199	Structure of the SANT domain from the Xenopus chromatin remodeling factor ISWI
Q27640567	Structure of the YibK methyltransferase from Haemophilus influenzae (HI0766): a cofactor bound at a site formed by a knot
Q53891195	Structure of the adenovirus E4 Orf6 protein predicted by fold recognition and comparative protein modeling
Q27663525	Structure of the amino-terminal domain from the cell-cycle regulator Swi6
Q27642616	Structure of the bacillus subtilis YYCN protein: a putative N-acetyltransferase
Q27668191	Structure of the catalytic domain of glucuronoyl esterase Cip2 from Hypocrea jecorina
Q30157142	Structure of the heme/hemoglobin outer membrane receptor ShuA from Shigella dysenteriae: heme binding by an induced fit mechanism
Q27687647	Structure of the hypothetical protein Ton1535 from Thermococcus onnurineus NA1 reveals unique structural properties by a left-handed helical turn in normal α-solenoid protein
Q28138164	Structure of the integral membrane domain of the GLP1 receptor
Q29540751	Structure of the integral membrane domain of the GLP1 receptor
Q27650275	Structure of the partially unliganded met state of 400 kDa hemoglobin: insights into ligand-induced structural changes of giant hemoglobins
Q43269859	Structure of the ribosome associating GTPase HflX.
Q27620631	Structure of the small G protein Rap2 in a non-catalytic complex with GTP
Q27697457	Structure of the terminal PCP domain of the non-ribosomal peptide synthetase in teicoplanin biosynthesis
Q46500567	Structure of the tetrameric form of human L-Xylulose reductase: probing the inhibitor-binding site with molecular modeling and site-directed mutagenesis.
Q41087270	Structure of the yeast Bre1 RING domain.
Q34060201	Structure of trichosanthin at 1.88 A resolution
Q30176590	Structure prediction and fold recognition for the ferrochelatase family of proteins
Q28250601	Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home
Q30380039	Structure prediction for CASP8 with all-atom refinement using Rosetta.
Q38339608	Structure prediction of a complex between the chromosomal protein HMG-D and DNA.
Q91487322	Structure prediction of biological assemblies using GALAXY in CAPRI rounds 38-45
Q30384246	Structure prediction using sparse simulated NOE restraints with Rosetta in CASP11.
Q88417944	Structure refinement of membrane proteins via molecular dynamics simulations
Q85198369	Structure refinement of protein model decoys requires accurate side‐chain placement
Q27860657	Structure validation by Calpha geometry: phi,psi and Cbeta deviation
Q46803209	Structure, conformational stability, and enzymatic properties of acylphosphatase from the hyperthermophile Sulfolobus solfataricus
Q30155826	Structure, dynamics, and Hck interaction of full-length HIV-1 Nef.
Q27650763	Structure, dynamics, and binding thermodynamics of the v-Src SH2 domain: implications for drug design
Q34988155	Structure, dynamics, and interactions of jacalin. Insights from molecular dynamics simulations examined in conjunction with results of X-ray studies
Q71074649	Structure, energetics, and dynamics of lipid-protein interactions: A molecular dynamics study of the gramicidin A channel in a DMPC bilayer
Q44544349	Structure, evolution, and inhibitor interaction of S-adenosyl-L-homocysteine hydrolase from Plasmodium falciparum
Q27645454	Structure, flexibility, and mechanism of the Bacillus stearothermophilus RecU Holliday junction resolvase
Q31473053	Structure-based analysis of protein dynamics: comparison of theoretical results for hen lysozyme with X-ray diffraction and NMR relaxation data
Q27650762	Structure-based approach to pharmacophore identification, in silico screening, and three-dimensional quantitative structure-activity relationship studies for inhibitors of Trypanosoma cruzi dihydrofolate reductase function
Q37222972	Structure-based classification of 45 FK506-binding proteins
Q51540257	Structure-based classification of FAD binding sites: A comparative study of structural alignment tools.
Q33366003	Structure-based design of a T-cell receptor leads to nearly 100-fold improvement in binding affinity for pepMHC.
Q74464016	Structure-based design of model proteins
Q40594026	Structure-based identification of binding sites, native ligands and potential inhibitors for G-protein coupled receptors.
Q34975441	Structure-based identification of catalytic residues.
Q47890169	Structure-based inhibitor screening: a family of sulfonated dye inhibitors for malaria parasite triosephosphate isomerase.
Q27694678	Structure-based investigation into the functional roles of the extended loop and substrate-recognition sites in an endo-β-1,4-D-mannanase from the Antarctic springtail, Cryptopygus antarcticus
Q52206940	Structure-based ligand design by dynamically assembling molecular building blocks at binding site
Q81003129	Structure-based mutagenesis of Penicillium griseofulvum xylanase using computational design
Q30321828	Structure-based prediction of DNA target sites by regulatory proteins.
Q47596442	Structure-based prediction of DNA-binding sites on proteins using the empirical preference of electrostatic potential and the shape of molecular surfaces
Q51891629	Structure-based prediction of transcription factor binding sites using a protein-DNA docking approach
Q27644505	Structure-based protein engineering for alpha-amylase inhibitory activity of plant defensin
Q30588355	Structure-based simulations reveal concerted dynamics of GPCR activation
Q33326721	Structure-based tailoring of compound libraries for high-throughput screening: discovery of novel EphB4 kinase inhibitors
Q52250455	Structure-based thermodynamic design of peptide ligands: Application to peptide inhibitors of the aspartic protease endothiapepsin
Q33285015	Structure-based virtual ligand screening with LigandFit: pose prediction and enrichment of compound collections
Q45277435	Structure-based, biophysical annotation of molecular coevolution of acetylcholinesterase
Q40137005	Structure-function relationship of inhibitory Smads: Structural flexibility contributes to functional divergence
Q44072534	Structure-function relationships in 3-phosphoglycerate kinase: role of the carboxy-terminal peptide
Q34713855	Structure-function relationships in the 2-oxo acid dehydrogenase family: substrate-specific signatures and functional predictions for the 2-oxoglutarate dehydrogenase-like proteins
Q35943452	Structure-function relationships of the hematopoietic growth factors
Q38310374	Structure-guided analysis of catalytic specificity of the abundantly secreted chitosanase SACTE_5457 from Streptomyces sp. SirexAA-E.
Q43823211	Structure-guided approach for detecting large domain inserts in protein sequences as illustrated using the haloacid dehalogenase superfamily.
Q41927287	Structure-guided forcefield optimization
Q87482896	Structure-kinetic relationship of carbapenem antibacterials permeating through E. coli OmpC porin
Q42676940	Structure/function of KRAB repression domains: structural properties of KRAB modules inferred from hydrodynamic, circular dichroism, and FTIR spectroscopic analyses.
Q34325473	Structured disorder and conformational selection
Q90403222	Structures and activities of widely conserved small prokaryotic aminopeptidases-P clarify classification of M24B peptidases
Q38971732	Structures and recognition modes of toll-like receptors
Q92372224	Structures of Hsp90α and Hsp90β bound to a purine-scaffold inhibitor reveal an exploitable residue for drug selectivity
Q83898714	Structures of N-acetylornithine transcarbamoylase from Xanthomonas campestris complexed with substrates and substrate analogs imply mechanisms for substrate binding and catalysis
Q27650471	Structures of a potent phenylalkyl bisphosphonate inhibitor bound to farnesyl and geranylgeranyl diphosphate synthases
Q27696880	Structures of citrate synthase and malate dehydrogenase of Mycobacterium tuberculosis
Q46800884	Structures of complexes of rhizopuspepsin with pepstatin and other statine-containing inhibitors
Q27646881	Structures of dimeric dihydrodiol dehydrogenase apoenzyme and inhibitor complex: probing the subunit interface with site-directed mutagenesis
Q82649959	Structures of intact glycoproteins from vibrational circular dichroism
Q52360845	Structures of jacalin-related lectin PPL3 regulating pearl shell biomineralization.
Q57095150	Structures of mesophilic and extremophilic citrate synthases reveal rigidity and flexibility for function
Q27704889	Structures of paraoxon-inhibited human acetylcholinesterase reveal perturbations of the acyl loop and the dimer interface
Q27666632	Structures of parasitic CDPK domains point to a common mechanism of activation
Q27687968	Structures of reduced and ligand-bound nitric oxide reductase provide insights into functional differences in respiratory enzymes
Q40760197	Structures of scrambled disulfide forms of the potato carboxypeptidase inhibitor predicted by molecular dynamics simulations with constraints
Q57957053	Structures of scrambled disulfide forms of the potato carboxypeptidase inhibitor predicted by molecular dynamics simulations with constraints
Q30159690	Structures of soluble amyloid oligomers from computer simulations
Q27731983	Structures of the "open" and "closed" state of trypanosomal triosephosphate isomerase, as observed in a new crystal form: implications for the reaction mechanism
Q27660306	Structures of the autoproteolytic domain from theSaccharomyces cerevisiaenuclear pore complex component, Nup145
Q27654471	Structures of twoArabidopsis thalianamajor latex proteins represent novel helix-grip folds
Q43852590	Structures of vertebrate hyaluronidases and their unique enzymatic mechanism of hydrolysis
Q27684611	Structure‐based engineering of streptavidin monomer with a reduced biotin dissociation rate
Q43502365	Structure‐based prediction of protein–peptide specificity in rosetta
Q30361792	Studies of the molten globule state of ferredoxin: structural characterization and implications on protein folding and iron-sulfur center assembly.
Q73427999	Studies of the unfolding of an unstable mutant of staphylococcal nuclease: evidence for low temperature unfolding and compactness of the high temperature unfolded state
Q28267131	Studies of the zein-like alpha-prolamins based on an analysis of amino acid sequences: implications for their evolution and three-dimensional structure
Q30396151	Studies on the inference of protein binding regions across fold space based on structural similarities
Q27745686	Studies on the inhibitor-binding site of porcine aldehyde reductase: Crystal structure of the holoenzyme-inhibitor ternary complex
Q45832587	Study of Q224K, V152G double mutation in bean PGIP2, an LRR protein for plant defense—An in silico approach
Q52306154	Study of global motions in proteins by weighted masses molecular dynamics: adenylate kinase as a test case
Q51970529	Study of protein-protein interaction using conformational space annealing
Q51985235	Study of the Villin headpiece folding dynamics by combining coarse-grained Monte Carlo evolution and all-atom molecular dynamics
Q52133646	Study of the electrostatics treatment in molecular dynamics simulations
Q33347927	Study of the impact of the T877A mutation on ligand-induced helix-12 positioning of the androgen receptor resulted in design and synthesis of novel antiandrogens
Q46634376	Study of the insulin dimerization: binding free energy calculations and per-residue free energy decomposition
Q99603107	Studying dynamics without explicit dynamics: a structure-based study of the export mechanism by AcrB
Q48229799	Studying pressure denaturation of a protein by molecular dynamics simulations
Q33671898	Studying submicrosecond protein folding kinetics using a photolabile caging strategy and time-resolved photoacoustic calorimetry.
Q47586066	Sub-angstrom modeling of complexes between flexible peptides and globular proteins.
Q34163319	Subcellular location prediction of apoptosis proteins
Q44060658	Subdomains in the F and G helices of bacteriorhodopsin regulate the conformational transitions of the reprotonation mechanism
Q46022091	Substrate binding modifies the hinge bending characteristics of human 3-phosphoglycerate kinase: a molecular dynamics study.
Q44745620	Substrate binding to mononuclear metallo-beta-lactamase from Bacillus cereus
Q46393912	Substrate directs enzyme dynamics by bridging distal sites: UDP-galactopyranose mutase
Q27633262	Substrate flow in catalases deduced from the crystal structures of active site variants of HPII from Escherichia coli
Q41917068	Substrate induced structural and dynamics changes in human phosphomevalonate kinase and implications for mechanism.
Q68137851	Substrate mobility in a deeply buried active site: analysis of norcamphor bound to cytochrome P-450cam as determined by a 201-psec molecular dynamics simulation
Q58456703	Substrate polarization in enzyme catalysis: QM/MM analysis of the effect of oxaloacetate polarization on acetyl-CoA enolization in citrate synthase
Q54720062	Substrate recognition by the EcoRI endonuclease.
Q46142968	Substrate specificities in class A beta-lactamases: preference for penams vs. cephems. The role of residue 237.
Q36129891	Substrate specificity characterization for eight putative nudix hydrolases. Evaluation of criteria for substrate identification within the Nudix family
Q51188485	Substrate specificity in HIV-1 protease by a biased sequence search method
Q39846885	Substrate stereo-specificity in tryptophan dioxygenase and indoleamine 2,3-dioxygenase.
Q28081510	Substrate tunnels in enzymes: structure-function relationships and computational methodology
Q30381183	Substrate uptake and protein stability relationship in mammalian histidine decarboxylase.
Q50996579	Substrate versus inhibitor dynamics of P-glycoprotein
Q93056725	Substrate-dependent transport mechanism in AcrB of multidrug resistant bacteria
Q62648718	Substrate-enzyme interactions and catalytic mechanism in phospholipase C: A molecular modeling study using the GRID program
Q46896541	Substrate-free structure of a monomeric NADP isocitrate dehydrogenase: an open conformation phylogenetic relationship of isocitrate dehydrogenase
Q57752101	Substrate-mediated control of the conformation of an ancillary domain delivers a competent catalytic site for N-acetylneuraminic acid synthase
Q44359047	Substrate-shielding and hydrolytic reaction in hydrolases.
Q82863059	Substructural cooperativity and parallel versus sequential events during protein unfolding
Q73876909	Subtle functional collective motions in pancreatic-like ribonucleases: from ribonuclease A to angiogenin
Q44379436	Subunit E of mitochondrial ATP synthase: a bioinformatic analysis reveals a phosphopeptide binding motif supporting a multifunctional regulatory role and identifies a related human brain protein with the same motif
Q45212617	Subunit assembly and active site location in the structure of glutamate dehydrogenase
Q54768950	Subunit assembly and metabolic stability of E. coli RNA polymerase.
Q52281049	Successful ab initio prediction of the tertiary structure of NK‐lysin using multiple sequences and recognized supersecondary structural motifs
Q52015252	Successful discrimination of protein interactions
Q43765189	Successful molecular dynamics simulation of two zinc complexes bridged by a hydroxide in phosphotriesterase using the cationic dummy atom method
Q57000512	Successful prediction of the coiled coil geometry of the GCN4 leucine zipper domain by simulated annealing: Comparison to the X-ray structure
Q30424396	Successful protein fold recognition by optimal sequence threading validated by rigorous blind testing
Q52141257	Successful recognition of protein folds using threading methods biased by sequence similarity and predicted secondary structure
Q51728577	Sucrose prevents protein fibrillation through compaction of the tertiary structure but hardly affects the secondary structure.
Q42620563	Super folds, networks, and barriers
Q28143898	Super-motifs and evolution of tandem leucine-rich repeats within the small proteoglycans--biglycan, decorin, lumican, fibromodulin, PRELP, keratocan, osteoadherin, epiphycan, and osteoglycin
Q58023176	Superantigen natural affinity maturation revealed by the crystal structure of staphylococcal enterotoxin G and its binding to T-cell receptor Vβ8.2
Q46035013	Superfamily active site templates.
Q51929016	Surface hydrophobic groups, stability, and flip-flopping in lattice proteins
Q68033367	Surface interactions of gamma-crystallins in the crystal medium in relation to their association in the eye lens
Q30422345	Surface motifs by a computer vision technique: searches, detection, and implications for protein-ligand recognition
Q52229473	Surface properties of adipocyte lipid-binding protein: Response to lipid binding, and comparison with homologous proteins
Q80867938	Surface recognition elements of membrane protein oligomerization
Q39869782	Surface shapes and surrounding environment analysis of single- and double-stranded DNA-binding proteins in protein-DNA interface
Q42054429	Surface-based protein binding pocket similarity
Q74419058	Surface-exposed phenylalanines in the RNP1/RNP2 motif stabilize the cold-shock protein CspB from Bacillus subtilis
Q39865644	Surface‐histogram: A new shape descriptor for protein‐protein docking
Q44544345	Survey for g-proteins in the prokaryotic genomes: prediction of functional roles based on classification
Q30821888	Survey of phosphorylation near drug binding sites in the Protein Data Bank (PDB) and their effects
Q51632243	Survey of the geometric association of domain-domain interfaces
Q44060644	Susceptibility to proteolysis of triosephosphate isomerase from two pathogenic parasites: characterization of an enzyme with an intact and a nicked monomer
Q40793518	Sustained performance of knowledge-based potentials in fold recognition.
Q60229708	Swapping the domains of exoribonucleases RNase II and RNase R: Conferring upon RNase II the ability to degrade ds RNA
Q52036909	Swaps in protein sequences
Q51328754	Swfoldrate: Predicting protein folding rates from amino acid sequence with sliding window method
Q35161189	SymmRef: a flexible refinement method for symmetric multimers
Q30382391	Symmetry-restrained molecular dynamics simulations improve homology models of potassium channels
Q41300612	Synergistic enhancement of cellulase pairs linked by consensus ankyrin repeats: Determination of the roles of spacing, orientation, and enzyme identity
Q45270047	Synthetic peptides corresponding to sequences of snake venom neurotoxins and rabies virus glycoprotein bind to the nicotinic acetylcholine receptor
Q81268383	System for accepting server predictions in CASP6
Q29547923	Systematic analysis of domain motions in proteins from conformational change: New results on citrate synthase and T4 lysozyme
Q81979762	Systematic classification of CDR-L3 in antibodies: implications of the light chain subtypes and the VL-VH interface
Q79236327	Systematic comparison of catalytic mechanisms of hydrolysis and transfer reactions classified in the EzCatDB database
Q30396232	Systematic evaluation of CS-Rosetta for membrane protein structure prediction with sparse NOE restraints
Q30371090	Systematic solution to homo-oligomeric structures determined by NMR.
Q27655054	Systematic structural studies of iron superoxide dismutases from human parasites and a statistical coupling analysis of metal binding specificity
Q40353250	TASSER-based refinement of NMR structures
Q51963686	TASSER: an automated method for the prediction of protein tertiary structures in CASP6.
Q30391461	TASSER_low-zsc: an approach to improve structure prediction using low z-score-ranked templates
Q39644236	THz frequency spectrum of protein-solvent interaction energy using a recurrence plot-based Wiener-Khinchin method
Q91460855	TKSA-MC: A web server for rational mutation through the optimization of protein charge interactions
Q30392295	TMSEG: Novel prediction of transmembrane helices
Q30336234	TOUCHSTONE: a unified approach to protein structure prediction.
Q30336124	TOUCHSTONEX: protein structure prediction with sparse NMR data.
Q27647821	TPR domain of NrfG mediates complex formation between heme lyase and formate-dependent nitrite reductase in Escherichia coli O157:H7
Q51547005	TSAR, a new graph–theoretical approach to computational modeling of protein side‐chain flexibility: Modeling of ionization properties of proteins
Q112582210	Tackling Covid-19 using disordered-to-order transition of residues in the spike protein upon angiotensin-converting enzyme 2 binding
Q81307659	Taking advantage of local structure descriptors to analyze interresidue contacts in protein structures and protein complexes
Q47613348	Taking geometry to its edge: fast unbound rigid (and hinge-bent) docking
Q42115423	Talin-driven inside-out activation mechanism of platelet αIIbβ3 integrin probed by multimicrosecond, all-atom molecular dynamics simulations
Q85889966	Tamoxifen, an anticancer drug, is an activator of human aldehyde dehydrogenase 1A1
Q27649292	Tandem use of X-ray crystallography and mass spectrometry to obtain ab initio the complete and exact amino acids sequence of HPBP, a human 38-kDa apolipoprotein
Q24647352	Target domain definition and classification in CASP8
Q41928117	Target highlights from the first post-PSI CASP experiment (CASP12, May-August 2016).
Q92816927	Target highlights in CASP13: Experimental target structures through the eyes of their authors
Q30408519	Target highlights in CASP9: Experimental target structures for the critical assessment of techniques for protein structure prediction
Q46436407	Target selection and deselection at the Berkeley Structural Genomics Center
Q42582837	Targeted molecular dynamics reveals overall common conformational changes upon hybrid domain swing-out in beta3 integrins
Q34618181	Targeted molecular dynamics simulation studies of binding and conformational changes in E. coli MurD.
Q30731629	Targeting novel folds for structural genomics
Q54729743	Targeting the conformational transitions of MDM2 and MDMX: insights into key residues affecting p53 recognition.
Q53297291	Targeting the early steps of Abeta16-22 protofibril disassembly by N-methylated inhibitors: a numerical study
Q51570059	Tat peptide‐calmodulin binding studies and bioinformatics of HIV‐1 protein–calmodulin interactions
Q38289496	Taxonomic distribution, repeats, and functions of the S1 domain-containing proteins as members of the OB-fold family.
Q52575406	Tchebichef image moment approach to the prediction of protein secondary structures based on circular dichroism
Q34284914	Temperature and pressure denaturation of chignolin: Folding and unfolding simulation by multibaric‐multithermal molecular dynamics method
Q87486112	Temperature and pressure effects on C112S azurin: volume, expansivity, and flexibility changes
Q48420779	Temperature dependence of the NMR generalized order parameter
Q30164200	Temperature dependence of the free energy landscape of the src-SH3 protein domain
Q43982440	Temperature effects on the hydrodynamic radius of the intrinsically disordered N-terminal region of the p53 protein
Q47107100	Temperature stability of proteins: Analysis of irreversible denaturation using isothermal calorimetry.
Q87957424	Temperature-accelerated molecular dynamics gives insights into globular conformations sampled in the free state of the AC catalytic domain
Q33326719	Temperature-dependent downhill unfolding of ubiquitin. I. Nanosecond-to-millisecond resolved nonlinear infrared spectroscopy
Q52586107	Temperature-dependent downhill unfolding of ubiquitin. II. Modeling the free energy surface
Q82665031	Temperature-dependent oligomerization in M-crystallin: lead or lag toward cataract, an NMR perspective
Q81075444	Temperature-dependent structural and functional features of a hyperthermostable enzyme using elastic neutron scattering
Q45816549	Temperature-dependent study reveals that dynamics of hydrophobic residues plays an important functional role in the mitochondrial Tim9-Tim10 complex.
Q52378057	Temperature-induced complementarity as a mechanism for biomolecular assembly
Q47771272	Temperature-induced partially unfolded state of hUBF HMG Box-5: conformational and dynamic investigations of the Box-5 thermal intermediate ensemble
Q47402752	Temperature-induced unfolding behavior of proteins studied by tensorial elastic network model
Q27675987	Temperature‐dependent conformational change affecting Tyr11 and sweetness loops of brazzein
Q30378664	Template based protein structure modeling by global optimization in CASP11.
Q30380289	Template-based and free modeling by RAPTOR++ in CASP8
Q47589415	Template-based and free modeling of I-TASSER and QUARK pipelines using predicted contact maps in CASP12.
Q47567198	Template-based modeling and ab initio refinement of protein oligomer structures using GALAXY in CAPRI round 30.
Q90388648	Template-based modeling and ab-initio docking using CoDock in CAPRI
Q30364787	Template-based modeling and free modeling by I-TASSER in CASP7.
Q92838113	Template-based modeling by ClusPro in CASP13 and the potential for using co-evolutionary information in docking
Q91163154	Template-based modeling of diverse protein interactions in CAPRI rounds 38-45
Q30409791	Template-based protein structure modeling using TASSER(VMT.).
Q30378816	Template-based protein structure prediction in CASP11 and retrospect of I-TASSER in the last decade.
Q47361532	Template-based quaternary structure prediction of proteins using enhanced profile-profile alignments.
Q30380345	Template-free modeling by LEE and LEER in CASP11.
Q30376832	Template-free protein structure prediction and quality assessment with an all-atom free-energy model.
Q84677897	Tensorial elastic network model for protein dynamics: Integration of the anisotropic network model with bond‐bending and twist elasticities
Q82521398	Terminal ion pairs stabilize the second beta-hairpin of the B1 domain of protein G
Q34389239	Terminal sialic acids on CD44 N-glycans can block hyaluronan binding by forming competing intramolecular contacts with arginine sidechains
Q82365981	Terminal-group effects on the folding behavior of selected beta-peptides
Q58008929	Tertiary and quaternary conformational changes in aspartate transcarbamylase: a normal mode study
Q30431726	Tertiary structure prediction of mixed alpha/beta proteins via energy minimization
Q46172421	Tertiary structure prediction of the KIX domain of CBP using Monte Carlo simulations driven by restraints derived from multiple sequence alignments
Q68082931	Test of circular dichroism (CD) methods for crambin and CD-assisted secondary structure prediction of its homologous toxins
Q47810344	Testing a new Monte Carlo algorithm for protein folding
Q58042939	Testing a new Monte Carlo algorithm for protein folding
Q34579607	Testing computational prediction of missense mutation phenotypes: functional characterization of 204 mutations of human cystathionine beta synthase
Q58042924	Testing similarity measures with continuous and discrete protein models
Q34774496	Tethering polypeptides through bifunctional PEG cross-linking agents to probe protein function: application to ATP synthase
Q30160179	The "first in-last out" hypothesis on protein folding revisited
Q30322866	The "random-coil" state of proteins: comparison of database statistics and molecular simulations.
Q47588389	The (non)malignancy of cancerous amino acidic substitutions
Q27648274	The 1.3 A crystal structure of a novel endo-beta-1,3-glucanase of glycoside hydrolase family 16 from alkaliphilic Nocardiopsis sp. strain F96
Q27649474	The 1.38 Å crystal structure of DmsD protein fromSalmonella typhimurium, a proofreading chaperone on the Tat pathway
Q47714920	The 1.59 A resolution crystal structure of TM0096, a flavin mononucleotide binding protein from Thermotoga maritima
Q57572230	The 1.6-Å resolution crystal structure of NovW: A 4-keto-6-deoxy sugar epimerase from the novobiocin biosynthetic gene cluster of Streptomyces spheroides
Q69537537	The 15 N-terminal amino acids of hexokinase II are not required for in vivo function: analysis of a truncated form of hexokinase II in Saccharomyces cerevisiae
Q27656125	The 2.1 Å crystal structure of an acyl-CoA synthetase from Methanosarcina acetivorans reveals an alternate acyl-binding pocket for small branched acyl substrates
Q27685454	The 2/2 hemoglobin from the cyanobacterium Synechococcus sp. PCC 7002 with covalently attached heme: comparison of X-ray and NMR structures
Q93012343	The 3A6-TCR/superagonist/HLA-DR2a complex shows similar interface and reduced flexibility compared to the complex with self-peptide
Q58428627	The 4th meeting on the Critical Assessment of Predicted Interaction (CAPRI) held at the Mare Nostrum, Barcelona
Q41958187	The ABC transporters in Candidatus Liberibacter asiaticus
Q96162993	The Actin cytoskeleton orchestra in Entamoeba histolytica
Q45070142	The B-ring substituent at C-7 of colchicine and the alpha-C-terminus of tubulin communicate through the "tail-body" interaction
Q73303306	The C-terminal domain of HPII catalase is a member of the type I glutamine amidotransferase superfamily
Q50701620	The C-terminal domain of the transcriptional regulator BldD from Streptomyces coelicolor A3(2) constitutes a novel fold of winged-helix domains
Q41931296	The C-terminal extension of human RTEL1, mutated in Hoyeraal-Hreidarsson syndrome, contains harmonin-N-like domains.
Q38347632	The C-terminal module of Chi1 from Aeromonas caviae CB101 has a function in substrate binding and hydrolysis
Q43023799	The C-terminal region of thermophilic tRNA (m7G46) methyltransferase (TrmB) stabilizes the dimer structure and enhances fidelity of methylation
Q27860601	The CCPN data model for NMR spectroscopy: development of a software pipeline
Q81481796	The CDR1 of the human lambdaVI light chains adopts a new canonical structure
Q83844462	The Caenorhabditis elegans DAF-12 nuclear receptor: structure, dynamics, and interaction with ligands
Q30349877	The ConSurf-HSSP database: the mapping of evolutionary conservation among homologs onto PDB structures.
Q98774561	The Crystal Structure of AbsH3: a Putative FAD-dependent Reductase in the Abyssomicin Biosynthesis Pathway
Q30440962	The DC-module of doublecortin: dynamics, domain boundaries, and functional implications
Q68236075	The DNA replication inhibitor microcin B17 is a forty-three-amino-acid protein containing sixty percent glycine
Q27650257	The Escherichia coli YdcF binds S-adenosyl-L-methionine and adopts an alpha/beta-fold characteristic of nucleotide-utilizing enzymes
Q91244924	The GluN2B-Glu413Gly NMDA receptor variant arising from a de novo GRIN2B mutation promotes ligand-unbinding and domain opening
Q80380717	The Gō model revisited: Native structure and the geometric coupling between local and long-range contacts
Q42339476	The H3 loop of antibodies shows unique structural characteristics
Q27640180	The HI0073/HI0074 protein pair from Haemophilus influenzae is a member of a new nucleotidyltransferase family: structure, sequence analyses, and solution studies
Q41937609	The HIV-1 p66 homodimeric RT exhibits different conformations in the binding-competent and -incompetent NNRTI site
Q41673312	The Helicobacter pylori genome: from sequence analysis to structural and functional predictions
Q27648703	The HhH domain of the human DNA repair protein XPF forms stable homodimers
Q33229210	The Histone Database: a comprehensive resource for histones and histone fold-containing proteins
Q28295769	The N- and C-termini of the human Nogo molecules are intrinsically unstructured: bioinformatics, CD, NMR characterization, and functional implications
Q43420513	The N-terminal domains of SOCS proteins: a conserved region in the disordered N-termini of SOCS4 and 5.
Q88046683	The N-terminal of annexin A1 as a secondary membrane binding site: a molecular dynamics study
Q30394771	The NMR solution structure and function of RPA3313: a putative ribosomal transport protein from Rhodopseudomonas palustris
Q27650668	The NMR solution structure of the artificial protein M7 matches the computationally designed model
Q27667929	The PR/SET domain in PRDM4 is preceded by a zinc knuckle
Q33225808	The Protein Circular Dichroism Data Bank (PCDDB): a bioinformatics and spectroscopic resource
Q30845175	The Protein Coil Library: a structural database of nonhelix, nonstrand fragments derived from the PDB.
Q43120115	The Rho GTPase inactivation domain in Vibrio cholerae MARTX toxin has a circularly permuted papain-like thiol protease fold
Q27704656	The SCP2-thiolase-like protein (SLP) of Trypanosoma brucei is an enzyme involved in lipid metabolism
Q31101733	The SHS2 module is a common structural theme in functionally diverse protein groups, like Rpb7p, FtsA, GyrI, and MTH1598/TM1083 superfamilies.
Q51906056	The SKE-DOCK server and human teams based on a combined method of shape complementarity and free energy estimation
Q44973571	The ST pinch: A side chain‐to‐side chain hydrogen‐bonded motif
Q91325485	The Short-chain Dehydrogenase/Reductase Engineering Database (SDRED): A classification and analysis system for a highly diverse enzyme family
Q52714241	The Structure of the N-terminal Module of the Cell Wall Hydrolase RipA and its Role in Regulating Catalytic Activity.
Q30406909	The VSGB 2.0 model: a next generation energy model for high resolution protein structure modeling
Q80949357	The X-ray crystal structure of PA3566 from Pseudomonas aureginosa at 1.8 A resolution
Q27646873	The X-ray crystallographic structure and activity analysis of a Pseudomonas-specific subfamily of the HAD enzyme superfamily evidences a novel biochemical function
Q27649513	The X-ray structure of N-methyltryptophan oxidase reveals the structural determinants of substrate specificity
Q27674962	The X‐ray crystallographic structure and specificity profile of HAD superfamily phosphohydrolase BT1666: Comparison of paralogous functions in B. thetaiotaomicron
Q57975285	The active-inactive transition of human thymidylate synthase: Targeted molecular dynamics simulations
Q45172676	The activity of recombinant human neuroglobin as an antioxidant and free radical scavenger
Q27663401	The adaptability of the active site of trypanosomal triosephosphate isomerase as observed in the crystal structures of three different complexes
Q48268370	The adaptive nature of protein residue networks.
Q30355437	The addition of 2,2,2-trifluoroethanol prevents the aggregation of guanidinium around protein and impairs its denaturation ability: a molecular dynamics simulation study.
Q46014933	The aggregation state of spin-labeled melittin in solution and bound to phospholipid membranes: evidence that membrane-bound melittin is monomeric.
Q113301902	The amounts of thermal vibrations and static disorder in protein X‐ray crystallographic B‐factors
Q39114591	The anatomy of mammalian sweet taste receptors
Q27655448	The ankyrin repeat domain of Huntingtin interacting protein 14 contains a surface aromatic cage, a potential site for methyl-lysine binding
Q34432278	The anti-HIV cyanovirin-N domain is evolutionarily conserved and occurs as a protein module in eukaryotes.
Q45990153	The application of different solvation and electrostatic models in molecular dynamics simulations of ubiquitin: how well is the X-ray structure "maintained"?
Q47715144	The architecture of the binding site in redox protein complexes: implications for fast dissociation
Q43963799	The balance between the rates of incorporation and pyrophosphorolytic removal influences the HIV-1 reverse transcriptase bypass of an abasic site with deoxy-, dideoxy-, and ribonucleotides
Q36508923	The barrier for proton transport in aquaporins as a challenge for electrostatic models: the role of protein relaxation in mutational calculations
Q27688110	The basic helix-loop-helix region of the transcriptional repressor hairy and enhancer of split 1 is preorganized to bind DNA
Q46587424	The betaalphabetaalphabeta elementary supersecondary structure of the Rossmann fold from porcine lactate dehydrogenase exhibits characteristics of a molten globule
Q48693717	The binding affinities of proteins interacting with the PDZ domain of PICK1.
Q27644272	The bioactive conformation of glucose-dependent insulinotropic polypeptide by NMR and CD spectroscopy
Q47810422	The biology workbench—A seamless database and analysis environment for the biologist
Q51900431	The blind search for the closed states of hinge-bending proteins.
Q68878431	The building of protein structures from alpha-carbon coordinates
Q44291548	The carboxyl terminal domain of Escherichia coli DNA topoisomerase I confers higher affinity to DNA.
Q38294044	The catalytic domain of a bacterial lytic transglycosylase defines a novel class of lysozymes
Q27670688	The catalytic domain of the germination-specific lytic transglycosylase SleB fromBacillus anthracisdisplays a unique active site topology
Q44379459	The catalytic mechanism of Drosophila alcohol dehydrogenase: evidence for a proton relay modulated by the coupled ionization of the active site Lysine/Tyrosine pair and a NAD+ ribose OH switch
Q84523995	The catch bond mechanism between von Willebrand factor and platelet surface receptors investigated by molecular dynamics simulations
Q47414206	The challenge of modeling protein assemblies: The CASP12-CAPRI experiment.
Q83319404	The chaperone activity of α-synuclein: Utilizing deletion mutants to map its interaction with target proteins
Q92816908	The characterization of pc-polylines representing protein backbones
Q46168045	The characterization of recombinant mouse glandular kallikreins from E. coli
Q30153299	The chloroplast outer envelope protein P39 in Arabidopsis thaliana belongs to the Omp85 protein family
Q30341944	The cis-Pro touch-turn: a rare motif preferred at functional sites.
Q27730728	The closed conformation of a highly flexible protein: the structure of E. coli adenylate kinase with bound AMP and AMPPNP
Q27650207	The complex structure of calmodulin bound to a calcineurin peptide
Q46917398	The confirmation of the denatured structure of pyrrolidone carboxyl peptidase under nondenaturing conditions: difference in helix propensity of two synthetic peptides with single amino acid substitution
Q34005469	The conformation of the extracellular binding domain of Death Receptor 5 in the presence and absence of the activating ligand TRAIL: a molecular dynamics study
Q30366947	The conformational plasticity of calmodulin upon calcium complexation gives a model of its interaction with the oedema factor of Bacillus anthracis.
Q30373438	The conservation profile of a protein bears the imprint of the molecule that is evolutionarily coupled to the protein.
Q51054355	The conserved Arg241-Glu439 salt bridge determines flexibility of the inositol 1,4,5-trisphosphate receptor binding core in the ligand-free state
Q80773472	The conserved salt bridge linking two C-terminal beta/alpha units in homodimeric triosephosphate isomerase determines the folding rate of the monomer
Q30196050	The construction of new proteins: V. A template-assembled synthetic protein (TASP) containing both a 4-helix bundle and beta-barrel-like structure
Q52407607	The contribution of cross‐links to protein stability: A normal mode analysis of the configurational entropy of the native state
Q40533640	The control of the discrimination between dNTP and rNTP in DNA and RNA polymerase
Q45070165	The coupling of structural fluctuations to hydride transfer in dihydrofolate reductase
Q27652356	The crystal structure and identification of NQM1/YGR043C, a transaldolase from Saccharomyces cerevisiae
Q34449680	The crystal structure of 5-keto-4-deoxyuronate isomerase from Escherichia coli
Q37471263	The crystal structure of Aq_328 from the hyperthermophilic bacteria Aquifex aeolicus shows an ancestral histone fold.
Q27694605	The crystal structure of BlmI as a model for nonribosomal peptide synthetase peptidyl carrier proteins
Q62448424	The crystal structure of CagS from theHelicobacter pyloripathogenicity island
Q27724705	The crystal structure of Clostridium perfringens SleM, a muramidase involved in cortical hydrolysis during spore germination
Q92514699	The crystal structure of Klebsiella pneumoniae FeoA reveals a site for protein-protein interactions
Q27660086	The crystal structure of NGO0477 from Neisseria gonorrhoeae reveals a novel protein fold incorporating a helix-turn-helix motif
Q27655518	The crystal structure of ORF14 from Sulfolobus islandicus filamentous virus
Q27684282	The crystal structure of Toxoplasma gondii nucleoside triphosphate diphosphohydrolase 1 represents a conformational intermediate in the reductive activation mechanism of the tetrameric enzyme
Q27646626	The crystal structure of Trypanosoma cruzi arginine kinase
Q27646808	The crystal structure of XC1258 from Xanthomonas campestris: a putative procaryotic Nit protein with an arsenic adduct in the active site
Q54459064	The crystal structure of XC1739: a putative multiple antibiotic-resistance repressor (MarR) from Xanthomonas campestris at 1.8 A resolution
Q79212149	The crystal structure of XC847 from Xanthomonas campestris: a 3'-5' oligoribonuclease of DnaQ fold family with a novel opposingly shifted helix
Q27658390	The crystal structure of XG-34, an evolved xyloglucan-specific carbohydrate-binding module
Q27644247	The crystal structure of a novel glucosamine-6-phosphate deaminase from the hyperthermophilic archaeon Pyrococcus furiosus
Q27695650	The crystal structure of archaeal serine hydroxymethyltransferase reveals idiosyncratic features likely required to withstand high temperatures
Q27633269	The crystal structure of chorismate lyase shows a new fold and a tightly retained product
Q27678874	The crystal structure of dihydrodipicolinate synthase from Escherichia coli with bound pyruvate and succinic acid semialdehyde: Unambiguous resolution of the stereochemistry of the condensation product
Q27649509	The crystal structure of human chloride intracellular channel protein 2: a disulfide bond with functional implications
Q27651940	The crystal structure of human cleavage and polyadenylation specific factor-5 reveals a dimeric Nudix protein with a conserved catalytic site
Q46980209	The crystal structure of human muscle glycogen phosphorylase a with bound glucose and AMP: an intermediate conformation with T-state and R-state features
Q27685506	The crystal structure of human quinolinic acid phosphoribosyltransferase in complex with its inhibitor phthalic acid
Q83340987	The crystal structure of hypothetical methyltransferase from Thermus thermophilus HB8
Q89110173	The crystal structure of maleylacetate reductase from Rhizobium sp. strain MTP-10005 provides insights into the reaction mechanism of enzymes in its original family
Q45902485	The crystal structure of methenyltetrahydromethanopterin cyclohydrolase from Methanobrevibacter ruminantium.
Q27617726	The crystal structure of recombinant rat pancreatic RNase A
Q27663117	The crystal structure of ribonuclease A in complex with thymidine-3'-monophosphate provides further insight into ligand binding
Q27652694	The crystal structure of staphylococcal nuclease refined at 1.7 A resolution
Q27663395	The crystal structure of the "open" and the "closed" conformation of the flexible loop of trypanosomal triosephosphate isomerase
Q27651180	The crystal structure of the ING5 PHD finger in complex with an H3K4me3 histone peptide
Q27645226	The crystal structure of the catalytic domain of the chick retinal neurite inhibitor-receptor protein tyrosine phosphatase CRYP-2/cPTPRO
Q27697433	The crystal structure of the catalytic domain of the ser/thr kinase PknA from M. tuberculosis shows an Src-like autoinhibited conformation
Q27647399	The crystal structure of the effector-binding domain of the trehalose repressor TreR from Bacillus subtilis 168 reveals a unique quarternary assembly
Q27648763	The crystal structure of the estA protein, a virulence factor from Streptococcus pneumoniae
Q91945231	The crystal structure of the mycobacterial trehalose monomycolate transport factor A, TtfA, reveals an atypical fold
Q27655516	The crystal structure of the outer membrane lipoprotein YbhC from Escherichia coli sheds new light on the phylogeny of carbohydrate esterase family 8
Q27650877	The crystal structure of the protein YhaK from Escherichia coli reveals a new subclass of redox sensitive enterobacterial bicupins
Q27644820	The crystal structure of the secreted aspartic proteinase 3 from Candida albicans and its complex with pepstatin A
Q27728484	The crystal structure of the ternary complex of staphylococcal nuclease, Ca2+, and the inhibitor pdTp, refined at 1.65 A
Q27620626	The crystal structure of triosephosphate isomerase (TIM) from Thermotoga maritima: a comparative thermostability structural analysis of ten different TIM structures
Q27694669	The crystal structure of type III effector protein XopQ from Xanthomonas oryzae complexed with adenosine diphosphate ribose
Q27651341	The crystal structures of the psychrophilic subtilisin S41 and the mesophilic subtilisin Sph reveal the same calcium-loaded state
Q41652276	The cytidylyltransferase superfamily: identification of the nucleotide-binding site and fold prediction
Q52237306	The dependence of amino acid pair correlations on structural environment
Q30195923	The design of idealized alpha/beta-barrels: analysis of beta-sheet closure requirements.
Q46122649	The design, synthesis, and crystallization of an alpha-helical peptide
Q30377801	The determinants of bond angle variability in protein/peptide backbones: A comprehensive statistical/quantum mechanics analysis.
Q44855339	The determinants of carboxyl pKa values in turkey ovomucoid third domain
Q46908446	The determinants of stability in the human prion protein: insights into folding and misfolding from the analysis of the change in the stabilization energy distribution in different conditions
Q30365569	The differences in the microenvironment of the two tryptophan residues of the glutamine-binding protein from Escherichia coli shed light on the binding properties and the structural dynamics of the protein.
Q27657486	The dimeric structure of Sulfolobus solfataricus thioredoxin A2 and the basis of its thermostability
Q88142617	The dimerization of PSGL-1 is driven by the transmembrane domain via a leucine zipper motif
Q30409630	The dual role of fragments in fragment-assembly methods for de novo protein structure prediction
Q52077265	The duplication of an eight-residue helical stretch in Staphylococcal nuclease is not helical: a model for evolutionary change
Q33384022	The effect of Asp54 phosphorylation on the energetics and dynamics in the response regulator protein Spo0F studied by molecular dynamics
Q30157049	The effect of calcium on the conformation of cobalamin transporter BtuB.
Q31150503	The effect of higher order RNA processes on changing patterns of protein domain selection: a developmentally regulated transcriptome of type 1 inositol 1,4,5-trisphosphate receptors
Q52209873	The effect of inhibitor binding on the structural stability and cooperativity of the HIV-1 protease
Q58616291	The effect of motional averaging on the calculation of NMR-derived structural properties
Q90607552	The effect of phosphate ion on the ssDNA binding mode of MoSub1, a Sub1/PC4 homolog from rice blast fungus
Q81547688	The effect of resolution-dependent global shape modifications on rigid-body protein-protein docking
Q68666383	The effect of solvent viscosity on the rate-determining step of fatty acid synthetase
Q39077397	The effect of specific proline residues on the kinetic stability of the triosephosphate isomerases of two trypanosomes.
Q42602581	The effects of rigid motions on elastic network model force constants
Q92952318	The effects of somatic mutations on EGFR interaction with anti-EGFR monoclonal antibodies: Implication for acquired resistance
Q83349839	The effects of the L29F mutation on the ligand migration kinetics in crystallized myoglobin as revealed by molecular dynamics simulations
Q52545512	The effects of truncating long-range forces on protein dynamics
Q46654279	The electrostatic potential of Escherichia coli dihydrofolate reductase
Q58106946	The elixir phase of chain molecules
Q31061756	The emergence of catalytic and structural diversity within the beta-clip fold
Q33902905	The energetics of the acetylation switch in p53-mediated transcriptional activation
Q37399868	The energy profiles of atomic conformational transition intermediates of adenylate kinase
Q42732147	The ensemble folding kinetics of the FBP28 WW domain revealed by an all‐atom Monte Carlo simulation in a knowledge‐based potential
Q52295098	The enthalpy change in protein folding and binding: refinement of parameters for structure-based calculations
Q72367448	The enzymatic mechanism of carboxypeptidase: a molecular dynamics study
Q58859753	The essential dynamics of thermolysin: Confirmation of the hinge-bending motion and comparison of simulations in vacuum and water
Q43027699	The esterase from the thermophilic eubacterium Bacillus acidocaldarius: structural-functional relationship and comparison with the esterase from the hyperthermophilic archaeon Archaeoglobus fulgidus.
Q50687502	The evolution and evolutionary consequences of marginal thermostability in proteins
Q82377300	The evolution of ATPase activity in SMC proteins
Q36580708	The evolution of function in strictosidine synthase-like proteins
Q33559060	The evolution of function within the Nudix homology clan
Q43556619	The evolutionary landscape of the chromatin modification machinery reveals lineage specific gains, expansions, and losses
Q30356675	The expanded FindCore method for identification of a core atom set for assessment of protein structure prediction.
Q44817543	The extended left-handed helix: a simple nucleic acid-binding motif
Q40914765	The family of the IL-6-type cytokines: specificity and promiscuity of the receptor complexes
Q48300024	The finite number of global motion patterns available to symmetric protein complexes.
Q27662232	The first crystal structure of an archaeal metallo-beta-lactamase superfamily protein; ST1585 from Sulfolobus tokodaii
Q27651125	The first high pH structure ofEscherichia coliaspartate transcarbamoylase
Q72321043	The first solvation shell of magnesium ion in a model protein environment with formate, water, and X-NH3, H2S, imidazole, formaldehyde, and chloride as ligands: an Ab initio study
Q41868069	The flexibility and dynamics of protein disulfide isomerase.
Q34102711	The flexible C-terminal arm of the Lassa arenavirus Z-protein mediates interactions with multiple binding partners
Q48629238	The folding funnel landscape for the peptide Met-enkephalin
Q46018101	The folding landscape of an alpha-lytic protease variant reveals the role of a conserved beta-hairpin in the development of kinetic stability.
Q50515281	The folding pathway of glycosomal triosephosphate isomerase: structural insights into equilibrium intermediates.
Q48100247	The fragment transformation method to detect the protein structural motifs
Q41685638	The free energies for mutating S27 and W79 to alanine in streptavidin and its biotin complex: the relative size of polar and nonpolar free energies on biotin binding
Q70125483	The frequency of ion-pair substructures in proteins is quantitatively related to electrostatic potential: a statistical model for nonbonded interactions
Q73233222	The function of conserved amino acid residues adjacent to the effector domain in elongation factor G
Q68704276	The galactan-binding immunoglobulin Fab J539: an X-ray diffraction study at 2.6-A resolution
Q34706258	The geometry of alpha-sheet: Implications for its possible function as amyloid precursor in proteins
Q79739100	The guanidino-group modifying enzymes: structural basis for their diversity and commonality
Q71537055	The heat capacity of proteins
Q50968912	The helix-coil transition revisited
Q42549663	The high-resolution crystal structure of a 24-kDa gyrase B fragment from E. coli complexed with one of the most potent coumarin inhibitors, clorobiocin
Q28255445	The high-resolution crystal structure of porcine pepsinogen
Q45249254	The human prion protein alpha2 helix: a thermodynamic study of its conformational preferences
Q92147375	The impact of different mutations at arginine141 on the structure, subunit exchange dynamics and chaperone activity of Hsp16.3.
Q57975302	The impact of protein flexibility on protein-protein docking
Q58213292	The impact of the fourth disulfide bridge in scorpion toxins of the α-KTx6 subfamily
Q46213311	The importance of explicit chain representation in protein folding models: An examination of ising‐like models
Q54214877	The influence of Mg2+ coordination on 13C and 15N chemical shifts in CKI1RD protein domain from experiment and molecular dynamics/density functional theory calculations
Q71623223	The influence of a protein on water dynamics in its vicinity investigated by molecular dynamics simulation
Q90300096	The influence of intrinsic folding mechanism of an unfolded protein on the coupled folding-binding process during target recognition
Q42229093	The influenza fusion peptide promotes lipid polar head intrusion through hydrogen bonding with phosphates and N-terminal membrane insertion depth
Q52687942	The insecticidal protein hirsutellin A from the mite fungal pathogen Hirsutella thompsonii is a ribotoxin
Q41875982	The interaction of calmodulin with fluorescent and photoreactive model peptides: evidence for a short interdomain separation
Q41761359	The interplay of structure and dynamics: insights from a survey of HIV-1 reverse transcriptase crystal structures.
Q34061894	The interprotein scoring noises in glide docking scores
Q31018067	The intracellular domain of the Drosophila cholinesterase-like neural adhesion protein, gliotactin, is natively unfolded.
Q80188310	The investigation of interactions of kappa-Hefutoxin1 with the voltage-gated potassium channels: a computational simulation
Q54702390	The isolation, purification, and preliminary crystallographic characterization of UDP-galactose-4-epimerase from Escherichia coli.
Q48155266	The key role of atom types, reference states, and interaction cutoff radii in the knowledge-based method: new variational approach
Q52263626	The kinetics of protein-protein recognition
Q42164209	The leghemoglobin proximal heme pocket directs oxygen dissociation and stabilizes bound heme.
Q40799777	The lifestyle of prokaryotic organisms influences the repertoire of promiscuous enzymes.
Q72589769	The limits of simulations
Q39864705	The linear interaction energy method for the prediction of protein stability changes upon mutation
Q71623218	The linker of calmodulin lacking Glu84 is elongated in solution, although it is bent in the crystal
Q33262338	The location and characterisation of the O-linked glycans of the human insulin receptor
Q48169004	The long unstructured region of Bcl-xl modulates its structural dynamics
Q44855345	The low barrier hydrogen bond (LBHB) proposal revisited: the case of the Asp... His pair in serine proteases
Q71543063	The magnitude of the backbone conformational entropy change in protein folding
Q46296762	The major toxin from the Australian Common Brown Snake is a hexamer with unusual gas-phase dissociation properties
Q41815499	The maturation of HIV-1 protease precursor studied by discrete molecular dynamics
Q42155548	The measured and calculated affinity of methyl- and methoxy-substituted benzoquinones for the Q(A) site of bacterial reaction centers
Q46476689	The mechanism of amyloid-fibril formation by stefin B: temperature and protein concentration dependence of the rates.
Q47342114	The mechanism of nucleotide-binding domain dimerization in the intact maltose transporter as studied by all-atom molecular dynamics simulations.
Q83013841	The mechanism of papain inhibition by peptidyl aldehydes
Q47867203	The mechanism of proton exclusion in aquaporin channels
Q36365074	The mechanism of the converter domain rotation in the recovery stroke of myosin motor protein.
Q27735412	The metal site of Pseudomonas aeruginosa azurin, revealed by a crystal structure determination of the Co(II) derivative and Co-EPR spectroscopy
Q46970759	The minimal α-crystallin domain of Mj Hsp16.5 is functional at non-heat-shock conditions
Q88006337	The modular structure of ThDP-dependent enzymes
Q88013870	The modules of trans-acyltransferase assembly lines redefined with a central acyl carrier protein
Q48043847	The molecular behavior of a single β-amyloid inside a dipalmitoylphosphatidylcholine bilayer at three different temperatures: An atomistic simulation study: Aβ interaction with DPPC: Atomistic simulation
Q51762113	The molecular evolution of HIV-1 protease simulated at atomic detail
Q47965368	The molecular mechanism behind resistance of the kinase FLT3 to the inhibitor quizartinib
Q44947540	The molecular origin of the thiamine diphosphate-induced spectral bands of ThDP-dependent enzymes.
Q34556266	The molecular structure of UDP-galactose 4-epimerase from Escherichia coli determined at 2.5 A resolution
Q30385457	The molten globule state as a clue for understanding the folding and cooperativity of globular-protein structure.
Q27652692	The mutation beta 99 Asp-Tyr stabilizes Y--a new, composite quaternary state of human hemoglobin
Q27643397	The mutations Lys 114 --> Gln and Asp 126 --> Asn disrupt an intersubunit salt bridge and convert Listeria innocua Dps into its natural mutant Listeria monocytogenes Dps. Effects on protein stability at Low pH
Q71623215	The native state of apomyoglobin described by proton NMR spectroscopy: the A-B-G-H interface of wild-type sperm whale apomyoglobin
Q43994829	The nature of intermolecular interactions between aromatic amino acid residues
Q53635588	The nature of the free energy barriers to two-state folding
Q28208426	The nature of the turn in omega loops of proteins
Q45076574	The nature of tryptophan radicals involved in the long-range electron transfer of lignin peroxidase and lignin peroxidase-like systems: Insights from quantum mechanical/molecular mechanics simulations
Q85889862	The near-symmetry of proteins
Q38211862	The neuraminidase of influenza virus
Q80867970	The noncatalytic triad of alpha-amylases: a novel structural motif involved in conformational stability
Q47589392	The nuclear DEK interactome supports multi-functionality.
Q47236457	The number of protein folds and their distribution over families in nature
Q44998319	The occurrence of C--H...O hydrogen bonds in alpha-helices and helix termini in globular proteins
Q47612425	The origin and extent of coarse-grained regularities in protein internal packing
Q46296772	The osmolyte betaine promotes protein misfolding and disruption of protein aggregates.
Q24604646	The other 90% of the protein: assessment beyond the Calphas for CASP8 template-based and high-accuracy models
Q35638699	The p66 immature precursor of HIV-1 reverse transcriptase.
Q37946320	The pKa Cooperative: A collaborative effort to advance structure‐based calculations of pKa values and electrostatic effects in proteins
Q38851416	The part of a long beta hairpin from the scrapie form of the human prion protein is reconstructed in the synthetic CC36 protein
Q52214244	The particle concept: placing discrete water molecules during protein-ligand docking predictions.
Q38297387	The peculiar structural features of kiwi fruit pectin methylesterase: amino acid sequence, oligosaccharides structure, and modeling of the interaction with its natural proteinaceous inhibitor
Q29615941	The penultimate rotamer library
Q56874662	The penultimate rotamer library
Q51906620	The performance of ZDOCK and ZRANK in rounds 6-11 of CAPRI.
Q87198984	The performance of fine-grained and coarse-grained elastic network models and its dependence on various factors
Q28267278	The peroxidase-cyclooxygenase superfamily: Reconstructed evolution of critical enzymes of the innate immune system
Q30192974	The phospho-beta-galactosidase and synaptotagmin predictions
Q83898721	The planar conformation of a strained proline ring: a QM/MM study
Q33310036	The point mutation A34F causes dimerization of GB1.
Q52066242	The prediction accuracy for protein structural class by the component-coupled method is around 60%.
Q40385795	The prediction of protein function at CASP6.
Q69544975	The pro-peptide is not necessary for active renin secretion from transfected mammalian cells
Q30366950	The protein fluorescence and structural toolkit: Database and programs for the analysis of protein fluorescence and structural data.
Q47307499	The protein target list of the Northeast Structural Genomics Consortium
Q47636226	The quaternary structure of carbonmonoxy hemoglobin ypsilanti
Q71313768	The rate-limiting step in the folding of the cis-Pro167Thr mutant of TEM-1 beta-lactamase is the trans to cis isomerization of a non-proline peptide bond
Q42831938	The reaction mechanism of type I phosphomannose isomerases: new information from inhibition and polarizable molecular mechanics studies
Q73319290	The reaction pathway of the isomerization of D-xylose catalyzed by the enzyme D-xylose isomerase: a theoretical study
Q57204650	The recognition of membrane-bound PtdIns3Pby PX domains
Q27678500	The reductive reaction mechanism of tobacco nitrite reductase derived from a combination of crystal structures and ultraviolet-visible microspectroscopy
Q27642082	The refined crystal structure of Pseudomonas putida lipoamide dehydrogenase complexed with NAD+ at 2.45 A resolution
Q42621654	The relationship between n-gram patterns and protein secondary structure
Q73594386	The relative order of helical propensity of amino acids changes with solvent environment
Q45264233	The repeat domain of the type III effector protein PthA shows a TPR-like structure and undergoes conformational changes upon DNA interaction.
Q51528062	The respective roles of polar/nonpolar binary patterns and amino acid composition in protein regular secondary structures explored exhaustively using hydrophobic cluster analysis.
Q42436318	The response of type three secretion system needle proteins MxiHDelta5, BsaLDelta5, and PrgIDelta5 to temperature and pH.
Q52626601	The restoration of electron micrographs blurred by drift and rotation
Q28288037	The role of Buergi-Dunitz interactions in the structural stability of proteins
Q58010827	The role of Li+, Na+, and K+ in the ligand binding inside the human acetylcholinesterase gorge
Q46634386	The role of Trp-82 in the folding of intestinal fatty acid binding protein
Q46872939	The role of a conserved histidine-tyrosine interhelical interaction in the ion channel domain of delta-endotoxins from Bacillus thuringiensis
Q46281486	The role of arginine 143 in the electrostatics and mechanism of Cu,Zn superoxide dismutase: computational and experimental evaluation by mutational analysis
Q35818865	The role of atomic level steric effects and attractive forces in protein folding
Q46857593	The role of backbone stability near Ala44 in the high reduction potential class of rubredoxins
Q30351181	The role of calcium in the conformational dynamics and thermal stability of the D-galactose/D-glucose-binding protein from Escherichia coli.
Q44784459	The role of carbon-donor hydrogen bonds in stabilizing tryptophan conformations
Q35631389	The role of conformational selection in the molecular recognition of the wild type and mutants XPA67-80 peptides by ERCC1.
Q41949035	The role of conserved water molecules in the catalytic domain of protein kinases
Q36071830	The role of domain: domain interactions versus domain: water interactions in the coarse-grained simulations of the E1P to E2P transitions in Ca-ATPase (SERCA).
Q44309138	The role of electrostatic interaction in the molecular recognition of selective agonists to metabotropic glutamate receptors
Q51463230	The role of electrostatics in TrxR electron transfer mechanism: A computational approach
Q73365490	The role of helix formation in the folding of a fully alpha-helical coiled coil
Q44060661	The role of hydrophobic microenvironments in modulating pKa shifts in proteins.
Q70604309	The role of local tight packing of hydrophobic groups in beta-structure
Q90483180	The role of negative selection in protein evolution revealed through the energetics of the native sate ensemble
Q30383783	The role of negative selection in protein evolution revealed through the energetics of the native state ensemble.
Q48007427	The role of pH on instability and aggregation of sickle hemoglobin solutions
Q31083553	The role of phosphorylation on the structure and dynamics of phospholamban: a model from molecular simulations
Q46865818	The role of residue stability in transient protein-protein interactions involved in enzymatic phosphate hydrolysis. A computational study
Q67505014	The role of tyrosine 67 in the cytochrome c heme crevice structure studied by semisynthesis
Q36623928	The role of tyrosine 71 in modulating the flap conformations of BACE1.
Q47974633	The role played by environmental residues on sidechain torsional angles within homologous families of proteins: a new method of sidechain modeling
Q56903322	The roles of residues Tyr150, Glu272, and His314 in class C beta-lactamases
Q37163585	The selenoproteome of Clostridium sp. OhILAs: characterization of anaerobic bacterial selenoprotein methionine sulfoxide reductase A
Q33316149	The size of the intermolecular energy funnel in protein-protein interactions
Q77669683	The slow step of folding of Staphylococcus aureus PC1 beta-lactamase involves the collapse of a surface loop rate limited by the trans to cis isomerization of a non-proline peptide bond
Q81044044	The solution structure of BmTx3B, a member of the scorpion toxin subfamily alpha-KTx 16
Q57755356	The solution structure of full-length dodecameric MCM by SANS and molecular modeling
Q39562819	The solution structure of the forkhead box-O DNA binding domain of Brugia malayi DAF-16a
Q27649510	The solution structure of the outer membrane lipoprotein OmlA from Xanthomonas axonopodis pv. citri reveals a protein fold implicated in protein-protein interaction
Q43019814	The stability of Taq DNA polymerase results from a reduced entropic folding penalty; identification of other thermophilic proteins with similar folding thermodynamics
Q30155110	The stability of cylindrin β-barrel amyloid oligomer models-a molecular dynamics study.
Q48254745	The starch-binding domain family CBM41-An in silico analysis of evolutionary relationships.
Q30339076	The state of the Protein Structure Initiative.
Q92822851	The structural details of the interaction of single-stranded DNA binding protein hSSB2 (NABP1/OBFC2A) with UV-damaged DNA
Q47307471	The structural genomics experimental pipeline: insights from global target lists.
Q79935413	The structural properties of magainin in water, TFE/water, and aqueous urea solutions: molecular dynamics simulations
Q27658328	The structure and NO binding properties of the nitrophorin-like heme-binding protein from Arabidopsis thaliana gene locus At1g79260.1
Q27661480	The structure of Boo/Diva reveals a divergent Bcl-2 protein
Q47310342	The structure of DLP12 endolysin exhibiting alternate loop conformation and comparative analysis with other endolysins
Q24311969	The structure of G117H mutant of butyrylcholinesterase: nerve agents scavenger
Q35085276	The structure of S. lividans acetoacetyl-CoA synthetase shows a novel interaction between the C-terminal extension and the N-terminal domain
Q27731286	The structure of Trypanosoma cruzi trypanothione reductase in the oxidized and NADPH reduced state
Q27667556	The structure of a D‐lyxose isomerase from the σB regulon of Bacillus subtilis
Q92331362	The structure of a GH149 β-(1 → 3) glucan phosphorylase reveals a new surface oligosaccharide binding site and additional domains that are absent in the disaccharide-specific GH94 glucose-β-(1 → 3)-glucose (laminaribiose) phosphorylase
Q34352233	The structure of a centrosymmetric protein crystal
Q27683455	The structure of a shellfish specific GST class glutathioneS‐transferase from antarctic bivalveLaternula ellipticareveals novel active site architecture
Q43023550	The structure of a thermally stable 3-phosphoglycerate kinase and a comparison with its mesophilic equivalent
Q34047792	The structure of aconitase
Q27648239	The structure of flavin-dependent tryptophan 7-halogenase RebH
Q28263368	The structure of murine neuroglobin: Novel pathways for ligand migration and binding
Q27664881	The structure of rubredoxin from Desulfovibrio desulfuricans strain 27774 at 1.5 A resolution
Q27643951	The structure of the Escherichia coli nucleoside diphosphate kinase reveals a new quaternary architecture for this enzyme family
Q27651127	The structure of the PP2A regulatory subunit B56 gamma: the remaining piece of the PP2A jigsaw puzzle
Q27650587	The structure of the anti-c-myc antibody 9E10 Fab fragment/epitope peptide complex reveals a novel binding mode dominated by the heavy chain hypervariable loops
Q27642166	The structure of the complex between influenza virus neuraminidase and sialic acid, the viral receptor
Q83349887	The structure of the ends of α-helices in globular proteins: effect of additional hydrogen bonds and implications for helix formation
Q91829246	The structure of the extended E2 DNA-binding domain of the bovine papillomavirus-1
Q27674964	The structure, molecular dynamics, and energetics of centrin-melittin complex
Q69444358	The surface area of monomeric proteins: significance of power law behavior
Q71543078	The surface of beta-sheet proteins contains amphiphilic regions which may provide clues about protein folding
Q30610407	The synthetase domains of cobalamin biosynthesis amidotransferases cobB and cobQ belong to a new family of ATP-dependent amidoligases, related to dethiobiotin synthetase
Q43000306	The targets of CAPRI Rounds 13-19.
Q47895843	The targets of CAPRI rounds 20–27
Q51970505	The targets of CAPRI rounds 3-5.
Q51909155	The targets of CAPRI rounds 6-12.
Q43018804	The thermal adaptation of the nitrogenase Fe protein from thermophilic Methanobacter thermoautotrophicus
Q30326370	The thermophilic esterase from Archaeoglobus fulgidus: structure and conformational dynamics at high temperature.
Q27620624	The three-dimensional solution structure of Aesculus hippocastanum antimicrobial protein 1 determined by 1H nuclear magnetic resonance
Q57831915	The three-dimensional solution structure ofAesculus hippocastanum antimicrobial protein 1 determined by1H nuclear magnetic resonance
Q27700901	The three-dimensional structure of "Lonely Guy" from Claviceps purpurea provides insights into the phosphoribohydrolase function of Rossmann fold-containing lysine decarboxylase-like proteins
Q42635059	The three-dimensional structure of Escherichia coli porphobilinogen deaminase at 1.76-A resolution
Q54702398	The three-dimensional structure of glutathione reductase from Escherichia coli at 3.0 A resolution.
Q27676234	The three-dimensional structure of recombinant bovine chymosin at 2.3 A resolution
Q44632574	The tissue factor/factor VIIa/factor Xa complex: a model built by docking and site-directed mutagenesis
Q57666117	The toxin-antitoxin proteins relBE2Spn of Streptococcus pneumoniae: Characterization and association to their DNA target
Q45855155	The translocation kinetics of antibiotics through porin OmpC: Insights from structure‐based solvation mapping using WaterMap
Q90907488	The tripartite architecture of the eukaryotic integral membrane protein zinc metalloprotease Ste24
Q47925510	The triterpene cyclase protein family: A systematic analysis
Q40135495	The type IA topoisomerase catalytic cycle: A normal mode analysis and molecular dynamics simulation
Q92926866	The uncharacterized bacterial protein YejG has the same architecture as domain III of elongation factor G
Q39023903	The unique N-terminal insert in the ribosomal protein, phosphoprotein P0, of Tetrahymena thermophila: Bioinformatic evidence for an interaction with 26S rRNA.
Q27641531	The unswapped chain of bovine seminal ribonuclease: Crystal structure of the free and liganded monomeric derivative
Q90564479	The unusual conformation of cross-strand disulfide bonds is critical to the stability of β-hairpin peptides
Q30379327	The use of automatic tools and human expertise in template-based modeling of CASP8 target proteins.
Q71267503	The use of position-specific rotamers in model building by homology
Q46428128	The utility of molecular dynamics simulations for understanding site-directed mutagenesis of glycine residues in biotin carboxylase
Q30378455	The value of protein structure classification information-Surveying the scientific literature.
Q40732945	The volume of cavities in proteins and virus capsids
Q27667775	The ygeW encoded protein from Escherichia coli is a knotted ancestral catabolic transcarbamylase
Q44859736	The α‐sheet: A missing‐in‐action secondary structure?
Q50103299	The ω-Transaminase Engineering Database (oTAED): A navigation tool in protein sequence and structure space
Q43599710	Theoretical evidence of a salt bridge disruption as the initiating process for the alpha1d-adrenergic receptor activation: a molecular dynamics and docking study
Q48061948	Theoretical insights into the protonation states of active site cysteine and citrullination mechanism of Porphyromonas gingivalis peptidylarginine deiminase.
Q59614298	Theoretical investigation of IL-6 multiprotein receptor assembly
Q44434505	Theoretical investigation on the diatomic ligand migration process and ligand binding properties in non‐O2‐binding H‐NOX domain
Q45172733	Theoretical investigations of prostatic acid phosphatase.
Q79364291	Theoretical model of human apolipoprotein B100 tertiary structure
Q30353106	Theoretical model of restriction endonuclease HpaI in complex with DNA, predicted by fold recognition and validated by site-directed mutagenesis.
Q53456582	Theoretical modeling of the O-intermediate structure of bacteriorhodopsin
Q70628268	Theoretical probes of conformational fluctuations in S-peptide and RNase A/3'-UMP enzyme product complex
Q70628274	Theoretical studies of relaxation of a monomeric subunit of HIV-1 protease in water using molecular dynamics
Q57991214	Theoretical studies on farnesyltransferase: The distances paradox explained
Q58008933	Theoretical study of the conformation of the H-protein lipoamide arm as a function of its terminal group
Q43765195	Theoretical study of the conformation of the lipoamide arm in a mutant H protein
Q42614803	Theoretical study of the electrostatically driven step of receptor-G protein recognition
Q59614258	Theoretical study of the electrostatically driven step of receptor-G protein recognition
Q44898269	Theoretical study of the ligand-CYP2B4 complexes: effect of structure on binding free energies and heme spin state
Q51777291	Theoretical tests of the mechanical protection strategy in protein nanomechanics
Q47974647	Theory of kinetic partitioning in protein folding with possible applications to prions
Q45838245	Thermal and acid denaturation of bovine lens α‐crystallin
Q51322092	Thermal denaturation of a recombinant mouse amelogenin: circular dichroism and differential scanning calorimetric studies
Q47307375	Thermal effects in stretching of Go-like models of titin and secondary structures
Q74721944	Thermal folding and mechanical unfolding pathways of protein secondary structures
Q36119188	Thermal green protein, an extremely stable, nonaggregating fluorescent protein created by structure-guided surface engineering.
Q27649817	Thermal stabilization of the protozoan Entamoeba histolytica alcohol dehydrogenase by a single proline substitution
Q42164230	Thermal unfolding molecular dynamics simulation of Escherichia coli dihydrofolate reductase: thermal stability of protein domains and unfolding pathway
Q30176191	Thermal unfolding of small proteins with SH3 domain folding pattern.
Q57831493	Thermal unfolding simulations of a multimeric protein-Transition state and unfolding pathways
Q52022848	Thermal unfolding simulations of apo-calmodulin using leap-dynamics
Q80218880	Thermal versus mechanical unfolding of ubiquitin
Q71460517	Thermally induced hydrogen exchange processes in small proteins as seen by FTIR spectroscopy
Q41294752	Thermitase, a thermostable subtilisin: comparison of predicted and experimental structures and the molecular cause of thermostability
Q73025534	Thermodynamic analysis of interactions between denaturants and protein surface exposed on unfolding: interpretation of urea and guanidinium chloride m-values and their correlation with changes in accessible surface area (ASA) using preferential inte
Q44867590	Thermodynamic analysis of structural transitions during GNNQQNY aggregation
Q34120049	Thermodynamic analysis of water molecules at the surface of proteins and applications to binding site prediction and characterization
Q51818471	Thermodynamic and kinetic characterization of a beta-hairpin peptide in solution: an extended phase space sampling by molecular dynamics simulations in explicit water.
Q54431818	Thermodynamic and kinetic determinants of Thermotoga maritima cold shock protein stability: a structural and dynamic analysis
Q27657789	Thermodynamic and structural analysis of highly stabilized BPTIs by single and double mutations
Q39000580	Thermodynamic and structural effect of urea and guanidine chloride on the helical and on a hairpin fragment of GB1 from molecular simulations
Q41980771	Thermodynamic basis of selectivity in guide‐target‐mismatched rna interference
Q54453983	Thermodynamic effects of proline introduction on protein stability.
Q44667169	Thermodynamic effects of replacements of Pro residues in helix interiors of maltose-binding protein
Q44193458	Thermodynamic genetics of the folding of the B1 immunoglobulin-binding domain from streptococcal protein G.
Q52404189	Thermodynamic integration calculations of binding free energy difference for Gly-169 mutation in subtilisin BPN'.
Q30386278	Thermodynamic resolution: how do errors in modeled protein structures affect binding affinity predictions?
Q41951688	Thermodynamic stability, unfolding kinetics, and aggregation of the N-terminal actin-binding domains of utrophin and dystrophin.
Q57835665	Thermodynamics and dynamics of amyloid peptide oligomerization are sequence dependent
Q85891722	Thermodynamics of Aβ16-21 dissociation from a fibril: Enthalpy, entropy, and volumetric properties
Q38896032	Thermodynamics of an aminoglycoside modifying enzyme with low substrate promiscuity: The aminoglycoside N3 acetyltransferase-VIa.
Q46163796	Thermodynamics of binding by calmodulin correlates with target peptide α-helical propensity
Q37019434	Thermodynamics of calmodulin binding to cardiac and skeletal muscle ryanodine receptor ion channels
Q44089217	Thermodynamics of ligand binding and denaturation for His64 mutants of tissue plasminogen activator kringle-2 domain
Q57966740	Thermodynamics of protein-cation interaction: Ca+2 and Mg+2 binding to the fifth binding module of the LDL receptor
Q40002852	Thermodynamics of the Trp-cage miniprotein unfolding in urea
Q31913230	Thermodynamics of the helix-coil transition: Binding of S15 and a hybrid sequence, disulfide stabilized peptide to the S-protein
Q30421277	Thermodynamics of ubiquitin unfolding
Q45383518	Thermodynamics of zinc binding to hepatitis C virus NS3 protease: a folding by binding event
Q33299335	Thermostable variants of the recombinant xylanase A from Bacillus subtilis produced by directed evolution show reduced heat capacity changes
Q41157648	Thiol protease-like active site found in the enzyme dienelactone hydrolase: Localization using biochemical, genetic, and structural tools
Q41144246	Thiol proteases and aldehyde dehydrogenases: Evolution from a common thiolesterase precursor?
Q43864564	Thioredoxin and peptide methionine sulfoxide reductase: convergence of similar structure and function in distinct structural folds
Q30424393	Threading a database of protein cores
Q43825557	Threading structural model of the manganese-stabilizing protein PsbO reveals presence of two possible beta-sandwich domains
Q30330077	Threading with chemostructural restrictions method for predicting fold and functionally significant residues: application to dipeptidylpeptidase IV (DPP-IV).
Q30794963	Threading with explicit models for evolutionary conservation of structure and sequence
Q57444423	Threading with explicit models for evolutionary conservation of structure and sequence
Q51886568	Threading without optimizing weighting factors for scoring function
Q44745622	Three acidic residues are at the active site of a beta-propeller architecture in glycoside hydrolase families 32, 43, 62, and 68.
Q33926211	Three enhancements to the inference of statistical protein‐DNA potentials
Q39325298	Three pairs of weak interactions precisely regulate the G-loop gate of Kir2.1 channel
Q57151709	Three ways in, one way out: Water dynamics in the trans‐membrane domains of the inner membrane translocase AcrB
Q45250514	Three-dimensional model of a substrate-bound SARS chymotrypsin-like cysteine proteinase predicted by multiple molecular dynamics simulations: catalytic efficiency regulated by substrate binding
Q61835565	Three-dimensional model of the SHBG-like region of anticoagulant protein S: New structure-function insights
Q43558045	Three-dimensional model of the SHBG-like region of anticoagulant protein S: new structure-function insights
Q30193062	Three-dimensional model of the alpha-subunit of bacterial luciferase
Q46881530	Three-dimensional model of the human aromatase enzyme and density functional parameterization of the iron-containing protoporphyrin IX for a molecular dynamics study of heme-cysteinato cytochromes.
Q46647178	Three-dimensional model of the human urotensin-II receptor: docking of human urotensin-II and nonpeptide antagonists in the binding site and comparison with an antagonist pharmacophore model
Q83358842	Three-dimensional modeling of cytomegalovirus DNA polymerase and preliminary analysis of drug resistance
Q36836475	Three-dimensional reconstruction of the hexagonal bilayer hemoglobin of the hydrothermal vent tube worm Riftia pachyptila by cryoelectron microscopy
Q57972072	Three-dimensional structural location and molecular functional effects of missense SNPs in the T cell receptor V? domain
Q45249259	Three-dimensional structure of GlcNAcalpha1-4Gal releasing endo-beta-galactosidase from Clostridium perfringens
Q27628948	Three-dimensional structure of a complex of galanthamine (Nivalin) with acetylcholinesterase from Torpedo californica: implications for the design of new anti-Alzheimer drugs
Q27694675	Three-dimensional structure of a fluorescein-Fab complex crystallized in 2-methyl-2,4-pentanediol
Q45831632	Three-dimensional structure of neuraminidase of subtype N9 from an avian influenza virus.
Q27698414	Three-dimensional structure of the neurotoxin ATX Ia from Anemonia sulcata in aqueous solution determined by nuclear magnetic resonance spectroscopy
Q44110878	Three-dimensional structure of the quinoprotein methylamine dehydrogenase from Paracoccus denitrificans determined by molecular replacement at 2.8 A resolution
Q42686073	Three-dimensional structure prediction of the NAD binding site of proton-pumping transhydrogenase from Escherichia coli
Q27664883	Three-dimensional structures of complexes of Lathyrus ochrus isolectin I with glucose and mannose: fine specificity of the monosaccharide-binding site
Q30414200	Three‐dimensional domain swapping in the protein structure space
Q57006875	Three‐dimensional model of the cyclin‐dependent kinase 1 (CDK1): Ab initio active site parameters for molecular dynamics studies of CDKS
Q37618717	Thumb inhibitor binding eliminates functionally important dynamics in the hepatitis C virus RNA polymerase
Q61587407	Tilted properties of the 67-78 fragment of α-synuclein are responsible for membrane destabilization and neurotoxicity
Q50518253	Time resolved fluorescence and phosphorescence properties of the individual tryptophan residues of barnase: evidence for protein-protein interactions
Q73025095	Time scale of protein aggregation dictated by liquid-liquid demixing
Q42545592	Time-dependent insulin oligomer reaction pathway prior to fibril formation: cooling and seeding
Q52040922	Time-resolved backbone desolvation and mutational hot spots in folding proteins
Q50750255	Time-resolved fluorescence study of a calcium-induced conformational change in prothrombin fragment 1.
Q56970636	Time‐resolved backbone desolvation and mutational hot spots in folding proteins
Q57975710	Titration_DB: Storage and analysis of NMR-monitored protein pH titration curves
Q46525599	Titration_DB: storage and analysis of NMR-monitored protein pH titration curves
Q33243877	Tolerance for random recombination of domains in prokaryotic and eukaryotic translation systems: Limited interdomain misfolding in a eukaryotic translation system
Q79319216	Tolerance to the substitution of buried apolar residues by charged residues in the homologous protein structures
Q42613952	Tomato pectin methylesterase: modeling, fluorescence, and inhibitor interaction studies-comparison with the bacterial (Erwinia chrysanthemi) enzyme
Q40653193	Topological and sequence information predict that foldons organize a partially overlapped and hierarchical structure
Q30344341	Topological determinants of protein unfolding rates.
Q30352985	Topological mirror images in protein structure computation: an underestimated problem.
Q47715221	Topological thermal instability and length of proteins
Q53079816	Topology‐based modeling of intrinsically disordered proteins: Balancing intrinsic folding and intermolecular interactions
Q28242162	Torsion angle dynamics: reduced variable conformational sampling enhances crystallographic structure refinement
Q30383777	Toward a detailed understanding of search trajectories in fragment assembly approaches to protein structure prediction
Q80465752	Toward a property/function relationship for metallothioneins: histidine coordination and unusual cluster composition in a zinc-metallothionein from plants
Q56889970	Toward a systems level view of the ECM and related proteins: a framework for the systematic definition and analysis of biological systems
Q51549010	Toward accurate prediction of pKa values for internal protein residues: The importance of conformational relaxation and desolvation energy
Q33206311	Toward an atomistic model for predicting transcription-factor binding sites
Q52077721	Toward an energy function for the contact map representation of proteins
Q42585482	Toward better refinement of comparative models: predicting loops in inexact environments
Q38950829	Toward decrypting the allosteric mechanism of the ryanodine receptor based on coarse-grained structural and dynamic modeling
Q38807269	Toward elucidating the heat activation mechanism of the TRPV1 channel gating by molecular dynamics simulation
Q24603390	Toward high-resolution homology modeling of antibody Fv regions and application to antibody-antigen docking
Q46713967	Toward minimalist models of larger proteins: a ubiquitin-like protein
Q30322873	Toward more meaningful hierarchical classification of protein three-dimensional structures.
Q30421206	Toward optimal fragment generations for ab initio protein structure assembly
Q36470740	Toward rational thermostabilization of Aspergillus oryzae cutinase: Insights into catalytic and structural stability
Q44910189	Toward the active conformations of rhodopsin and the beta2-adrenergic receptor
Q30342804	Toward the detection and validation of repeats in protein structure.
Q40231861	Toward the mechanism of dynamical couplings and translocation in hepatitis C virus NS3 helicase using elastic network model
Q84071518	Toward the quantum chemical calculation of nuclear magnetic resonance chemical shifts of proteins
Q38562658	Toward understanding the structure and interactions of microtubules and motor proteins
Q44960725	Towards a MIP-based alignment and docking in computer-aided drug design.
Q44947527	Towards a structural classification of phosphate binding sites in protein-nucleotide complexes: an automated all-against-all structural comparison using geometric matching
Q57936636	Towards a systems level view of the ECM and related proteins: A framework for the systematic definition and analysis of biological systems
Q30371811	Towards accurate residue-residue hydrophobic contact prediction for alpha helical proteins via integer linear optimization
Q27639345	Towards atomic resolution with crystals grown in gel: the case of thaumatin seen at room temperature
Q39743311	Towards computing with proteins.
Q33262339	Towards in silico lead optimization: scores from ensembles of protein/ligand conformations reliably correlate with biological activity
Q36825878	Towards meeting the Paracelsus Challenge: The design, synthesis, and characterization of paracelsin-43, an alpha-helical protein with over 50% sequence identity to an all-beta protein
Q40155467	Towards predicting Ca2+-binding sites with different coordination numbers in proteins with atomic resolution
Q45928897	Towards the elucidation of molecular determinants of cooperativity in the liver bile acid binding protein.
Q38308536	Towards the molecular understanding of glycogen elongation by amylosucrase
Q30394774	Towards understanding the crosstalk between protein post-translational modifications: Homo- and heterotypic PTM pair distances on protein surfaces are not random
Q34733126	Toxoplasma gondii ferredoxin-NADP+ reductase: Role of ionic interactions in stabilization of native conformation and structural cooperativity
Q27622556	Trans-substitution of the proximal hydrogen bond in myoglobin: I. Structural consequences of hydrogen bond deletion
Q73798364	Trans-substitution of the proximal hydrogen bond in myoglobin: II. Energetics, functional consequences, and implications for hemoglobin allostery
Q51899067	TransPath: a computational method for locating ion transit pathways through membrane proteins
Q58049054	Transcriptional activity of the TFIIA four-helix bundle in vivo
Q92174527	Transcriptional regulatory module analysis reveals that bridge proteins reconcile multiple signals in extracellular electron transfer pathways
Q73798381	Transcriptional repressor CopR: amino acids involved in forming the dimeric interface
Q73521268	Transcriptional repressor CopR: structure model-based localization of the deoxyribonucleic acid binding motif
Q27643366	Transformation of an alpha-helix peptide into a beta-hairpin induced by addition of a fragment results in creation of a coexisting state
Q130082615	Transient excited states of the metamorphic protein Mad2 and their implications for function
Q30159747	Transition state of a SH3 domain detected with principle component analysis and a charge-neutralized all-atom protein model
Q30163854	Transition states for folding of circular-permuted proteins
Q52313723	Translational regulation of ribosomal protein S15 drives characteristic patterns of protein-mRNA epistasis
Q68838759	Translational repression in vitro by the bacteriophage T4 regA protein
Q79402260	Trapping choline oxidase in a nonfunctional conformation by freezing at low pH
Q27652874	Trapping open and closed forms of FitE: a group III periplasmic binding protein
Q38662954	Treatment of electrostatic effects in macromolecular modeling
Q51652069	Treatment of electrostatic effects in proteins: multigrid-based Newton iterative method for solution of the full nonlinear Poisson-Boltzmann equation
Q44784448	Trehalose-protein interaction in aqueous solution
Q30165221	Triage protein fold prediction
Q39776843	Triathlon for energy functions: Who is the winner for design of protein–protein interactions?
Q41850711	Trifluoperazine regulation of calmodulin binding to Fas: A computational study
Q33587782	Trimethylamine N-oxide influence on the backbone of proteins: an oligoglycine model
Q80595869	Truncated prolyl oligopeptidase from Pyrococcus furiosus
Q38323413	Tryptophan microstate reshuffling upon the binding of cyclosporin A to human cyclophilin A.
Q46966110	Tryptophan side chain conformers monitored by NMR and time-resolved fluorescence spectroscopies
Q46463622	Tryptophan to phenylalanine substitutions allow differentiation of short- and long-range conformational changes during denaturation of goat alpha-lactalbumin
Q45028387	Tsp36, a tapeworm small heat-shock protein with a duplicated alpha-crystallin domain, forms dimers and tetramers with good chaperone-like activity
Q100695356	Tuning the binding interface between Machupo virus glycoprotein and human transferrin receptor
Q46167116	Tuning the conformational properties of the prion peptide
Q41717280	Turning a reference inside-out: commentary on an article by Stevens and Arkin entitled: "Are membrane proteins 'inside-out' proteins?" (Proteins 1999;36:135-143)
Q52077267	Turning an opinion inside-out: Rees and Eisenberg's commentary (Proteins 2000;38:121-122) on "Are membrane proteins 'inside-out' proteins?" (Proteins 1999;36:135-143).
Q45067684	Turning the growth hormone receptor on: evidence that hormone binding induces subunit rotation
Q42594652	Turns revisited: a uniform and comprehensive classification of normal, open, and reverse turn families minimizing unassigned random chain portions
Q79298613	Two alternative substrate paths for compound I formation and reduction in catalase-peroxidase KatG from Burkholderia pseudomallei
Q56877649	Two distinct heme distal site states define Cerebratulus lacteus mini-hemoglobin oxygen affinity
Q44817526	Two histidines of the coat protein of turnip yellow mosaic virus at the capsid interior are crucial for viability
Q27629371	Two mutants of human heparin binding protein (CAP37): toward the understanding of the nature of lipid A/LPS and BPTI binding
Q74363294	Two structural subdomains of barstar detected by rapid mixing NMR measurement of amide hydrogen exchange
Q68378966	Two trifluoperazine-binding sites on calmodulin predicted from comparative molecular modeling with troponin-C
Q46917650	Two types of transmembrane homomeric interactions in the integrin receptor family are evolutionarily conserved.
Q47702171	Two-domain analysis of JmjN-JmjC and PHD-JmjC lysine demethylases: Detecting an inter-domain evolutionary stress
Q40353256	Two-stage support vector regression approach for predicting accessible surface areas of amino acids
Q42985847	Two-state conformational equilibrium in the Par-4 leucine zipper domain.
Q75209201	Type I collagen N-telopeptides adopt an ordered structure when docked to their helix receptor during fibrillogenesis
Q43208253	UV and X-ray structural studies of a 101-residue long Tat protein from a HIV-1 primary isolate and of its mutated, detoxified, vaccine candidate
Q28262035	Ultrahigh resolution drug design I: details of interactions in human aldose reductase-inhibitor complex at 0.66 A
Q44898251	Ultrahigh resolution drug design. II. Atomic resolution structures of human aldose reductase holoenzyme complexed with Fidarestat and Minalrestat: implications for the binding of cyclic imide inhibitors
Q44464202	Ultraviolet illumination-induced reduction of alpha-lactalbumin disulfide bridges
Q80113376	Unambiguous prediction of human integrin transmembrane heterodimer interactions using only homologous sequences
Q53026162	Unbinding and unfolding of adhesion protein complexes through stretching: interplay between shear and tensile mechanical clamps
Q44157877	Unbinding free energy of acetylcholinesterase bound oxime drugs along the gorge pathway from metadynamics-umbrella sampling investigation
Q45028372	Unconventional interactions between water and heterocyclic nitrogens in protein structures
Q47700271	Uncovering allostery and regulation in SAMHD1 through molecular dynamics simulations
Q48099848	Uncovering allostery and regulation in SAMHD1 through molecular dynamics simulations
Q46823170	Understanding of known drug-target interactions in the catalytic pocket of neuraminidase subtype N1.
Q30331654	Understanding protein structure-function relationships in Family 47 alpha-1,2-mannosidases through computational docking of ligands.
Q37915098	Understanding structural relationships in proteins of unsolved three-dimensional structure
Q44566276	Understanding the acylation mechanisms of active-site serine penicillin-recognizing proteins: a molecular dynamics simulation study
Q41607608	Understanding the apparent stator-rotor connections in the rotary ATPase family using coarse-grained computer modeling
Q28709396	Understanding the basis of a class of paradoxical mutations in AraC through simulations
Q83782523	Understanding the binding mode and function of BMS-488043 against HIV-1 viral entry
Q30350005	Understanding the energetics of helical peptide orientation in membranes.
Q51068343	Understanding the folding and stability of a zinc finger-based full sequence design protein with replica exchange molecular dynamics simulations.
Q30384933	Understanding the physical basis for the side-chain conformational preferences of methionine.
Q47626965	Understanding the recognition of protein structural classes by amino acid composition
Q51924710	Understanding the regulation mechanisms of PAF receptor by agonists and antagonists: molecular modeling and molecular dynamics simulation studies
Q34011530	Understanding the role of Arg96 in structure and stability of green fluorescent protein
Q31155211	Understanding the roles of amino acid residues in tertiary structure formation of chignolin by using molecular dynamics simulation
Q81544592	Understanding the structural and functional differences between mouse thyrotropin-releasing hormone receptors 1 and 2
Q30341342	Unfolded state of polyalanine is a segmented polyproline II helix.
Q46794944	Unfolding and aggregation of transthyretin by the truncation of 50 N-terminal amino acids.
Q34747812	Unfolding energetics and stability of banana lectin.
Q30153467	Unfolding of beta-lactoglobulin on the surface of polystyrene nanoparticles: experimental and computational approaches
Q52540491	Unfolding of hen egg lysozyme by molecular dynamics simulations at 300K: insight into the role of the interdomain interface
Q30164435	Unfolding of the cold shock protein studied with biased molecular dynamics
Q31036143	Unfolding transition state and intermediates of the tumor suppressor p16INK4a investigated by molecular dynamics simulations.
Q42134646	Unifying mechanical and thermodynamic descriptions across the thioredoxin protein family.
Q28486499	Unique GMP-binding site in Mycobacterium tuberculosis guanosine monophosphate kinase
Q91142507	Unique active site formation in a novel galactose 1-phosphate uridylyltransferase from the hyperthermophilic archaeon Pyrobaculum aerophilum
Q27728033	Unique coenzyme binding mode of hyperthermophilic archaeal sn-glycerol-1-phosphate dehydrogenase from Pyrobaculum calidifontis
Q52082497	Unit-vector RMS (URMS) as a tool to analyze molecular dynamics trajectories
Q54487161	Universal biases in protein composition of model prokaryotes.
Q39924918	Universal features of fluctuations in globular proteins
Q57011846	Universality of protein reentrant condensation in solution induced by multivalent metal ions
Q27697928	Unprecedented access of phenolic substrates to the heme active site of a catalase: substrate binding and peroxidase-like reactivity of Bacillus pumilus catalase monitored by X-ray crystallography and EPR spectroscopy
Q64902463	Unraveling the mechanism of proton translocation in the extracellular half-channel of bacteriorhodopsin.
Q43245876	Unraveling the molecular basis for ligand binding in truncated hemoglobins: the trHbO Bacillus subtilis case
Q79838626	Unstructured intermediate states in single protein force experiments
Q46435560	Untangling influences of hydrophobicity on protein sequences and structures
Q73256218	Unusual amino acid usage in the variable regions of mercury-binding antibodies
Q45987978	Unusual zymogen-processing properties of a mutated form of prochymosin.
Q81282365	Unwinding the helical linker of calcium-loaded calmodulin: a molecular dynamics study
Q74566093	Urea effects on protein stability: Hydrogen bonding and the hydrophobic effect
Q27649057	Use of L-asparagine and N-phosphonacetyl-L-asparagine to investigate the linkage of catalysis and homotropic cooperativity in E. coli aspartate transcarbomoylase
Q41736263	Use of MM-PB/SA in estimating the free energies of proteins: application to native, intermediates, and unfolded villin headpiece
Q81318633	Use of bioinformatics tools for the annotation of disease-associated mutations in animal models
Q68115182	Use of conditional probabilities for determining relationships between amino acid sequence and protein secondary structure
Q52214942	Use of pair potentials across protein interfaces in screening predicted docked complexes
Q52234198	Use of quantitative structure-property relationships to predict the folding ability of model proteins
Q27701699	Use of restrained molecular dynamics in water to determine three-dimensional protein structure: prediction of the three-dimensional structure of Ecballium elaterium trypsin inhibitor II
Q39226773	Use of restrained molecular dynamics to predict the conformations of phosphorylated receiver domains in two-component signaling systems
Q30329265	Use of structure comparison methods for the refinement of protein structure predictions. I. Identifying the structural family of a protein from low-resolution models.
Q52256504	Use of the multiple copy simultaneous search (MCSS) method to design a new class of picornavirus capsid binding drugs
Q94655044	Using Machine Learning to Improve Ensemble Docking for Drug Discovery
Q104518300	Using Normal Mode Analysis on protein structural models. How far can we go on our predictions?
Q96162785	Using Restraints in EROS-Dock Improves Model Quality in Pairwise and Multicomponent Protein Docking
Q51152599	Using a consensus approach based on the conservation of inter-residue contacts to rank CAPRI models
Q43024386	Using a strategy based on the concept of convergent evolution to identify residue substitutions responsible for thermal adaptation
Q48094793	Using evolutionary and structural information to predict DNA-binding sites on DNA-binding proteins
Q45910840	Using evolutionary information for the query and target improves fold recognition.
Q34829661	Using genetic algorithms to select most predictive protein features
Q40130441	Using homology modeling to interrogate binding affinity in neutralization of ricin toxin by a family of single domain antibodies
Q54441169	Using molecular dynamics to map interaction networks in an aminoacyl-tRNA synthetase
Q79210002	Using multiple structure alignments, fast model building, and energetic analysis in fold recognition and homology modeling
Q45959093	Using physical potentials and learned models to distinguish native binding interfaces from de novo designed interfaces that do not bind
Q30366477	Using quantum mechanics to improve estimates of amino acid side chain rotamer energies
Q30365834	Using scores derived from statistical coupling analysis to distinguish correct and incorrect folds in de-novo protein structure prediction.
Q42051859	Using the concept of transient complex for affinity predictions in CAPRI rounds 20-27 and beyond
Q92431766	VH -VL interdomain dynamics observed by computer simulations and NMR
Q27745669	VL:VH domain rotations in engineered antibodies: crystal structures of the Fab fragments from two murine antitumor antibodies and their engineered human constructs
Q85097553	Validating and improving elastic network models with molecular dynamics simulations
Q33754209	Validating computer simulations of enantioselective catalysis; reproducing the large steric and entropic contributions in Candida Antarctica lipase B
Q35821952	Validating the vitality strategy for fighting drug resistance
Q52216406	Validation of NMR side-chain conformations by packing calculations
Q30402892	Validation of Protein Structure Models using Network Similarity Score
Q33625244	Validation of archived chemical shifts through atomic coordinates
Q58085189	Validation of chemical genetics for the study of zipper-interacting protein kinase signaling
Q47903272	Validation of nuclear magnetic resonance structures of proteins and nucleic acids: hydrogen geometry and nomenclature
Q36457575	Validation of the first step of the heuristic refinement method for the derivation of solution structures of proteins from NMR data
Q33855998	Variability in quaternary association of proteins with the same tertiary fold: a case study and rationalization involving legume lectins
Q44125134	Variability in the pKa of histidine side-chains correlates with burial within proteins
Q46044077	Variability of conformations at crystal contacts in BPTI represent true low-energy structures: correspondence among lattice packing and molecular dynamics structures
Q77192771	Variability of the canonical loop conformations in serine proteinases inhibitors and other proteins
Q30331168	Variants of 3(10)-helices in proteins.
Q47435943	Variation of folded polypeptide surface area with probe size
Q73784262	Variations on a theme by Debye and Waller: From simple crystals to proteins
Q30991459	Various strategies of using residual dipolar couplings in NMR-driven protein docking: application to Lys48-linked di-ubiquitin and validation against 15N-relaxation data
Q84966735	Versatile substrate protein recognition mechanism of the eukaryotic chaperonin CCT
Q29619767	Very fast empirical prediction and rationalization of protein pKa values
Q27144110	Very fast prediction and rationalization of pKa values for protein-ligand complexes
Q37130581	Very short peptides with stable folds: building on the interrelationship of Trp/Trp, Trp/cation, and Trp/backbone-amide interaction geometries
Q47214896	Vibrational entropy estimation can improve binding affinity prediction for non-obligatory protein complexes.
Q69837539	Vibrational spectroscopy of bacteriorhodopsin mutants: I. Tyrosine-185 protonates and deprotonates during the photocycle
Q44784445	Vicinal disulfide bridge conformers by experimental methods and by ab initio and DFT molecular computations
Q47596508	Virtual screening for inhibitors of human aldose reductase.
Q30365357	Virtual screening on an α-helix to β-strand switchable region of the FGFR2 extracellular domain revealed positive and negative modulators.
Q46607615	Virtual screening to enrich a compound collection with CDK2 inhibitors using docking, scoring, and composite scoring models
Q31120824	Virtual screening to enrich hit lists from high-throughput screening: a case study on small-molecule inhibitors of angiogenin.
Q34975702	Virtual screening using molecular simulations
Q73380010	Viscosity dependence of protein dynamics
Q45028380	Visualizing complexes of phospholipids with Streptomyces phospholipase D by automated docking
Q40369228	Visualizing global properties of a molecular dynamics trajectory
Q34488156	Vivaldi: visualization and validation of biomacromolecular NMR structures from the PDB.
Q30399505	VoroMQA: Assessment of protein structure quality using interatomic contact areas.
Q31031423	WHISCY: what information does surface conservation yield? Application to data-driven docking.
Q79739550	Walking through the protein sequence space: towards new generation of the homology modeling
Q40229014	Water and ion permeability of a claudin model: A computational study
Q45194394	Water dynamics simulation as a tool for probing proton transfer pathways in a heptahelical membrane protein
Q43986875	Water in protein cavities: A procedure to identify internal water and exchange pathways and application to fatty acid-binding protein
Q30587171	Water penetration and escape in proteins
Q57875300	Water penetration and escape in proteins
Q33298524	Water penetration in the low and high pressure native states of ubiquitin
Q61155774	Water transfer energetics and solid-like packing of globular proteins
Q27649512	Water-mediated interactions between DNA and PhoB DNA-binding/transactivation domain: NMR-restrained molecular dynamics in explicit water environment
Q30360721	WeFold: a coopetition for protein structure prediction
Q41182371	Weak correlation between predictive power of individual sequence patterns and overall prediction accuracy in proteins
Q46805508	Weak self-association of human growth hormone investigated by nitrogen-15 NMR relaxation.
Q77926223	Weak temperature dependence of the free energy surface and folding pathways of structured peptides
Q46569606	Weighing in on a Timeless controversy
Q47863740	Weighted geometric docking: incorporating external information in the rotation-translation scan
Q30382591	Wetting of nonconserved residue-backbones: A feature indicative of aggregation associated regions of proteins.
Q34325469	What are the dielectric "constants" of proteins and how to validate electrostatic models?
Q30352918	What determines the spectrum of protein native state structures?
Q41607783	What determines the van der Waals coefficient beta in the LIE (linear interaction energy) method to estimate binding free energies using molecular dynamics simulations?
Q90696602	What is life? Part II
Q30417147	What is the best reference state for designing statistical atomic potentials in protein structure prediction?
Q35531144	What is the pitch of the alpha-helical coiled coil?
Q30339077	What is the protein design alphabet?
Q30363271	What is the relationship between the global structures of apo and holo proteins?
Q30329568	What is the value added by human intervention in protein structure prediction?
Q47702142	What makes it difficult to refine protein models further via molecular dynamics simulations?
Q51718302	What stabilizes the 3(14)-helix in beta3-peptides? A conformational analysis using molecular simulation
Q42621329	When fold is not important: a common structural framework for adenine and AMP binding in 12 unrelated protein families
Q40645901	Where is NMR taking us?
Q29615739	Why are "natively unfolded" proteins unstructured under physiologic conditions?
Q102202336	Why are ACE2 binding coronavirus strains SARS-CoV/SARS-CoV-2 wild and NL63 mild?
Q47867220	Why are both ends of the polypeptide chain on the outside of proteins?
Q53950065	Why are polar residues within the membrane core evolutionary conserved?
Q71313752	Why are protein crystallographic R-values so high?
Q77360727	Why are proteins marginally stable?
Q70980700	Why do protein architectures have Boltzmann-like statistics?
Q86149583	Why does mutation of Gln61 in Ras by the nitro analog NGln maintain activity of Ras-GAP in hydrolysis of guanosine triphosphate?
Q30339075	Why does the Ras switch "break" by oncogenic mutations?
Q30361608	Why is the biological hydrophobicity scale more accurate than earlier experimental hydrophobicity scales?
Q77615171	Why protein R-factors are so large: a self-consistent analysis
Q46112510	Wild type and mutants of the HET-s(218-289) prion show different flexibility at fibrillar ends: a simulation study
Q45966211	Will my protein crystallize? A sequence-based predictor.
Q39640152	Wrapping mimicking in drug-like small molecules disruptive of protein-protein interfaces
Q51627898	X-ray absorption and molecular dynamics study of cation binding sites in the purple membrane.
Q27649049	X-ray analysis of phosphoglycerate kinase 2, a sperm-specific isoform from Mus musculus
Q68052812	X-ray and model-building studies on the specificity of the active site of proteinase K
Q72867734	X-ray crystal structure and molecular dynamics simulation of bovine pancreas phospholipase A2-n-dodecylphosphorylcholine complex
Q27642896	X-ray crystal structure of CutA from Thermotoga maritima at 1.4 Å resolution
Q27636876	X-ray crystal structure of MTH938 from Methanobacterium thermoautotrophicum at 2.2 A resolution reveals a novel tertiary protein fold
Q27677556	X-ray crystal structure of TTHB099, a CRP/FNR superfamily transcriptional regulator from Thermus thermophilus HB8, reveals a DNA-binding protein with no required allosteric effector molecule
Q27653536	X-ray crystal structure of a CRISPR-associated RAMP module [corrected] Cmr5 protein [corrected] from Thermus thermophilus HB8
Q27652192	X-ray crystal structure of a CRISPR-associated protein, Cse2, from Thermus thermophilus HB8
Q27649054	X-ray crystal structure of a hypothetical Sua5 protein from Sulfolobus tokodaii strain 7
Q40416001	X-ray crystal structure of cytochrome P450 monooxygenase CYP101J2 from Sphingobium yanoikuyae strain B2.
Q27649475	X-ray crystal structure of the B component of Hemolysin BL from Bacillus cereus
Q39032567	X-ray crystal structure of the N-terminal region of Moloney murine leukemia virus integrase and its implications for viral DNA recognition
Q27697881	X-ray crystal structures of an orally available aminopeptidase inhibitor, Tosedostat, bound to anti-malarial drug targets PfA-M1 and PfA-M17
Q79264650	X-ray crystal structures of the conserved hypothetical proteins from Arabidopsis thaliana gene loci At5g11950 and AT2g37210
Q41358072	X-ray crystal structures of the pheromone-binding domains of two quorum-hindered transcription factors, YenR of Yersinia enterocolitica and CepR2 of Burkholderia cenocepacia.
Q27656122	X-ray crystallographic studies of RNase A variants engineered at the most destabilizing positions of the main hydrophobic core: further insight into protein stability
Q27619066	X-ray crystallographic studies of the denaturation of ribonuclease S
Q27627412	X-ray crystallographic study of xylopentaose binding to Pseudomonas fluorescens xylanase A
Q27698099	X-ray crystallographic validation of structure predictions used in computational design for protein stabilization
Q44855351	X-ray structural and simulation analysis of a protein mutant: the value of a combined approach.
Q27655824	X-ray structure and kinetic properties of ornithine transcarbamoylase from the human parasiteGiardia lamblia
Q46634383	X-ray structure of Arabidopsis At1g77680, 12-oxophytodienoate reductase isoform 1.
Q45093334	X-ray structure of Arabidopsis At2g06050, 12-oxophytodienoate reductase isoform 3.
Q60913206	X-ray structure of HI0817 from Haemophilus influenzae: Protein of unknown function with a novel fold
Q27651624	X-ray structure of HIV-1 protease in situ product complex
Q27650791	X-ray structure of ILL2, an auxin-conjugate amidohydrolase fromArabidopsis thaliana
Q27638953	X-ray structure of Mycobacterium tuberculosis nucleoside diphosphate kinase
Q27639349	X-ray structure of Saccharomyces cerevisiae homologous mitochondrial matrix factor 1 (Hmf1)
Q42162700	X-ray structure of a domain-swapped dimer of Ser46-phosphorylated Crh from Bacillus subtilis.
Q38337174	X-ray structure of a membrane-bound beta-glycosidase from the hyperthermophilic archaeon Pyrococcus horikoshii
Q27640126	X-ray structure of an M. jannaschii DNA-binding protein: implications for antibiotic resistance in S. aureus
Q48007385	X-ray structure of human gankyrin, the product of a gene linked to hepatocellular carcinoma.
Q27646809	X-ray structure of imidazolonepropionase from Agrobacterium tumefaciens at 1.87 A resolution
Q27640901	X-ray structure of the T. Aquaticus Ftsy:GDP complex suggests functional roles for the C-terminal helix of the SRP GTPases
Q27653937	X-ray structure ofDanio reriosecretagogin: A hexa-EF-hand calcium sensor
Q27650206	X-ray structures of Sap1 and Sap5: structural comparison of the secreted aspartic proteinases from Candida albicans
Q27730538	X-ray structures of fragments from binding and nonbinding versions of a humanized anti-CD18 antibody: structural indications of the key role of VH residues 59 to 65
Q37319930	X-ray vs. NMR structures as templates for computational protein design.
Q27667218	X-ray, ESR, and quantum mechanics studies unravel a spin well in the cofactor-less urate oxidase
Q38337971	XANNpred: neural nets that predict the propensity of a protein to yield diffraction-quality crystals
Q27653355	XC1028 from Xanthomonas campestris adopts a PilZ domain-like structure without a c-di-GMP switch
Q27645230	XC5848, an ORFan protein from Xanthomonas campestris, adopts a novel variant of Sm-like motif
Q27655648	Xanthomonas campestris PqqD in the pyrroloquinoline quinone biosynthesis operon adopts a novel saddle-like fold that possibly serves as a PQQ carrier
Q30351133	YAKUSA: a fast structural database scanning method.
Q51184138	YASSPP: better kernels and coding schemes lead to improvements in protein secondary structure prediction
Q42629835	YbdK is a carboxylate-amine ligase with a gamma-glutamyl:Cysteine ligase activity: crystal structure and enzymatic assays.
Q45229449	YbiV from Escherichia coli K12 is a HAD phosphatase
Q43023486	YesT: a new rhamnogalacturonan acetyl esterase from Bacillus subtilis
Q81892390	ZDOCK and RDOCK performance in CAPRI rounds 3, 4, and 5
Q52015260	ZDOCK predictions for the CAPRI challenge
Q52015255	ZDOCK: an initial-stage protein-docking algorithm
Q51042892	ZRANK: reranking protein docking predictions with an optimized energy function
Q94958145	Zinc Binding Promotes Greater Hydrophobicity in Alzheimer's Aβ42 peptide than Copper Binding: Molecular Dynamics and Solvation Thermodynamics Studies
Q73798416	Zinc binding in bovine alpha-lactalbumin: sequence homology may not be a predictor of subtle functional features
Q58322019	Zinc binding in bovine α‐lactalbumin: Sequence homology may not be a predictor of subtle functional features
Q70830917	Zinc binding in proteins and solution: a simple but accurate nonbonded representation
Q81505336	Zinc binding of Tim10: evidence for existence of an unstructured binding intermediate for a zinc finger protein
Q46393926	Zn2+-linked dimerization of UreG from Helicobacter pylori, a chaperone involved in nickel trafficking and urease activation
Q34084053	alpha-helix formation: discontinuous molecular dynamics on an intermediate-resolution protein model
Q31623586	alpha-lactalbumin mutant acting as lysozyme
Q42638117	beta-fructosidase superfamily: homology with some alpha-L-arabinases and beta-D-xylosidases
Q96341897	cnnAlpha: Protein Disordered Regions Prediction by Reduced Amino Acid Alphabets and Convolutional Neural Networks
Q80773519	fRMSDPred: predicting local RMSD between structural fragments using sequence information
Q33496507	gCOMBINE: A graphical user interface to perform structure-based comparative binding energy (COMBINE) analysis on a set of ligand-receptor complexes
Q27675295	hCINAP is an atypical mammalian nuclear adenylate kinase with an ATPase motif: Structural and functional studies
Q43989926	i-Patch: interprotein contact prediction using local network information
Q85991852	iATTRACT: simultaneous global and local interface optimization for protein-protein docking refinement
Q51928346	iGibbs: improving Gibbs motif sampler for proteins by sequence clustering and iterative pattern sampling
Q57930409	iProtGly-SS: Identifying protein glycation sites using sequence and structure based features
Q62717281	iSEE: Interface structure, evolution, and energy-based machine learning predictor of binding affinity changes upon mutations
Q48465476	mAb806 binding to epidermal growth factor receptor: a computational study
Q27659271	p-Coumaric acid decarboxylase from Lactobacillus plantarum: structural insights into the active site and decarboxylation catalytic mechanism
Q52428977	pH dependence of 2,3-diphosphoglycerate binding to human hemoglobin A0 at 21.5 degrees C.
Q87617267	pH dependence of conformational fluctuations of the protein backbone
Q28728601	pH replica‐exchange method based on discrete protonation states
Q41445457	pH sensitivity of type III secretion system tip proteins
Q45356158	pH-dependent molecular dynamics of vesicular stomatitis virus glycoprotein G.
Q59600477	pH-dependent stability of the human ?-lactalbumin molten globule state: Contrasting roles of the 6?120 disulfide and the ?-subdomain at low and neutral pH
Q42021257	pH‐selective mutagenesis of protein–protein interfaces: In silico design of therapeutic antibodies with prolonged half‐life
Q73798398	pK(a) calculations for class C beta-lactamases: the role of Tyr-150
Q57135342	pK(a) calculations of calbindin D(9k): effects of Ca(2+) binding, protein dielectric constant, and ionic strength
Q42147734	pKa predictions for proteins, RNAs, and DNAs with the Gaussian dielectric function using DelPhi pKa.
Q42604431	pKa predictions with a coupled finite difference Poisson-Boltzmann and Debye-Hückel method.
Q48279984	pyDock scoring for the new modeling challenges in docking: Protein-peptide, homo-multimers, and domain-domain interactions
Q57132401	pyDock: electrostatics and desolvation for effective scoring of rigid-body protein-protein docking
Q38726560	α-chymotrypsin in water-acetone and water-dimethyl sulfoxide mixtures: Effect of preferential solvation and hydration.
Q96436273	β-Strand-mediated interactions of protein domains
Q57751875	β-strand twisting/bending in soluble and transmembrane β-barrel structures
Q44774734	π-π Stacking mediated drug-drug interactions in human CYP2E1.
Q53393543	ω-Turn: a novel β-turn mimic in globular proteins stabilized by main-chain to side-chain C−H···O interaction

P6981	ACNP journal ID	19739
		2276168
P8375	Crossref journal ID	22119
P1250	Danish Bibliometric Research Indicator (BFI) SNO/CNO	152967
P356	DOI	10.1002/(ISSN)1097-0134
P1058	ERA Journal ID	15253
P646	Freebase ID	/m/0czcddw
P236	ISSN	0887-3585
		1097-0134
P7363	ISSN-L	0887-3585
P1277	JUFO ID	65625
P1144	Library of Congress Control Number (LCCN) (bibliographic)	90655008
P1055	NLM Unique ID	8700181
P243	OCLC control number	13196210
P856	official website	http://onlinelibrary.wiley.com/journal/10.1002/(ISSN)1097-0134
		https://onlinelibrary.wiley.com/journal/10970134
		http://www.interscience.wiley.com/jpages/0887-3585/
P10283	OpenAlex ID	S121161810
P3181	OpenCitations bibliographic resource ID	31769
P7461	Publons journals/conferences ID	21240
P7662	Scilit journal ID	61594
P1156	Scopus source ID	14283
P12897	Wiley Online Library journal ID	10970134

P495	country of origin	United States	Q30
P1240	Danish Bibliometric Research Indicator level	1
P571	inception	1986-01-01
P8875	indexed in bibliographic review	Scopus	Q371467
		Science Citation Index Expanded	Q104047209
P407	language of work or name	English	Q1860
P921	main subject	protein	Q8054
P123	publisher	Wiley	Q1479654
P1813	short name	Proteins
P1680	subtitle	Structure, Function, and Bioinformatics
P1476	title	Proteins

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	Proteins (journal)	wikipedia
Persian (fa / Q9168)	پروتئینز (مجله)	wikipedia

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