Modeling of loops in protein structures (scientific article (publication date: September 2000))

cites work (P2860)

Q57904681	1H, 13C, 15N resonance assignments and fold verification of a circular permuted variant of the potent HIV-inactivating protein cyanovirin-N
Q37323043	2-(m-Azidobenzoyl)taxol binds differentially to distinct β-tubulin isotypes
Q33276638	A Caenorhabditis elegans wild type defies the temperature-size rule owing to a single nucleotide polymorphism in tra-3.
Q64251681	A Metadynamics-Based Protocol for the Determination of GPCR-Ligand Binding Modes
Q37128015	A Rac GTPase-activating protein, MgcRacGAP, is a nuclear localizing signal-containing nuclear chaperone in the activation of STAT transcription factors
Q30157881	A TolC-like protein is required for heterocyst development in Anabaena sp. strain PCC 7120
Q38739986	A Triazinone Derivative Inhibits HIV-1 Replication by Interfering with Reverse Transcriptase Activity
Q43158551	A Two-amino Acid Mutation Encountered in Duchenne Muscular Dystrophy Decreases Stability of the Rod Domain 23 (R23) Spectrin-like Repeat of Dystrophin.
Q28914715	A Web Resource for Standardized Benchmark Datasets, Metrics, and Rosetta Protocols for Macromolecular Modeling and Design
Q34249720	A combination of computational and experimental approaches identifies DNA sequence constraints associated with target site binding specificity of the transcription factor CSL.
Q27331774	A common model for cytokine receptor activation: combined scissor-like rotation and self-rotation of receptor dimer induced by class I cytokine
Q47787775	A comprehensive in silico analysis of huntingtin and its interactome
Q39522616	A comprehensive software suite for the analysis of cDNAs
Q53285459	A fold-recognition approach to loop modeling.
Q44953484	A fragment based method for modeling of protein segments into cryo-EM density maps
Q30838359	A functional genomics investigation of allelochemical biosynthesis in Sorghum bicolor root hairs
Q92546283	A knottin scaffold directs the CXC-chemokine-binding specificity of tick evasins
Q44392853	A leucine-rich repeat assembly approach for homology modeling of the human TLR5-10 and mouse TLR11-13 ectodomains
Q41579846	A membrane-inserted structural model of the yeast mitofusin Fzo1.
Q85003541	A method for conformational sampling of loops in proteins based on adiabatic decoupling and temperature or force scaling
Q30421377	A modular perspective of protein structures: application to fragment based loop modeling
Q30368476	A multi-template combination algorithm for protein comparative modeling.
Q35111697	A multiscale modeling approach to investigate molecular mechanisms of pseudokinase activation and drug resistance in the HER3/ErbB3 receptor tyrosine kinase signaling network
Q64077828	A new benchmark illustrates that integration of geometric constraints inferred from enzyme reaction chemistry can increase enzyme active site modeling accuracy
Q33412232	A new prediction strategy for long local protein structures using an original description
Q34543373	A new structural framework for integrating replication protein A into DNA processing machinery.
Q24315833	A noncoding expansion in EIF4A3 causes Richieri-Costa-Pereira syndrome, a craniofacial disorder associated with limb defects
Q36897684	A novel mechanism by which thiazolidinediones facilitate the proteasomal degradation of cyclin D1 in cancer cells
Q42150684	A novel proton transfer mechanism in the SLC11 family of divalent metal ion transporters
Q30451175	A photochemical approach to the lipid accessibility of engineered cysteinyl residues
Q47982909	A report of rifampin-resistant leprosy from northern and eastern India: identification and in silico analysis of molecular interactions
Q29048167	A resource for benchmarking the usefulness of protein structure models
Q30621214	A robust all-atom model for LCAT generated by homology modeling
Q30379997	A self-organizing algorithm for modeling protein loops.
Q36583382	A single residue substitution accounts for the significant difference in thermostability between two isoforms of human cytosolic creatine kinase
Q39674136	A small difference in the molecular structure of angiotensin II receptor blockers induces AT1 receptor-dependent and -independent beneficial effects
Q37421771	A small molecule blocking oncogenic protein EWS-FLI1 interaction with RNA helicase A inhibits growth of Ewing's sarcoma
Q47070812	A structural basis for half-of-the-sites metal binding revealed in Drosophila melanogaster porphobilinogen synthase
Q34481883	A structural model for facultative anion channels in an oligomeric membrane protein: the yeast TRK (K(+)) system
Q46576648	A structural model for microtubule minus-end recognition and protection by CAMSAP proteins
Q42600411	A structural model for the open conformation of the mdr1 P-glycoprotein based on the MsbA crystal structure
Q33240022	A supersecondary structure library and search algorithm for modeling loops in protein structures
Q35740999	A three-dimensional model of human organic anion transporter 1: aromatic amino acids required for substrate transport
Q27683887	A unique Oct4 interface is crucial for reprogramming to pluripotency
Q44144384	A very large C-loop in EGF domain IV is characteristic of the P28 family of ookinete surface proteins
Q46944188	A wheat SIMILAR TO RCD-ONE gene enhances seedling growth and abiotic stress resistance by modulating redox homeostasis and maintaining genomic integrity
Q34729910	A zebrafish in vivo phenotypic assay to identify 3-aminothiophene-2-carboxylic acid-based angiogenesis inhibitors
Q28114985	ADP-ribose-derived nuclear ATP synthesis by NUDIX5 is required for chromatin remodeling
Q30401875	AESOP: A Python Library for Investigating Electrostatics in Protein Interactions.
Q34183005	ASTRO-FOLD: A Combinatorial and Global Optimization Framework for Ab Initio Prediction of Three-Dimensional Structures of Proteins from the Amino Acid Sequence
Q30416167	AWSEM-MD: protein structure prediction using coarse-grained physical potentials and bioinformatically based local structure biasing
Q51961295	Ab initio construction of all-atom loop conformations.
Q33284072	Ab initio modeling of small proteins by iterative TASSER simulations
Q49264202	Ab initio modeling of small, medium, and large loops in proteins.
Q36260709	Accessing gap-junction channel structure-function relationships through molecular modeling and simulations
Q37073551	Accommodation of an N-(deoxyguanosin-8-yl)-2-acetylaminofluorene adduct in the active site of human DNA polymerase iota: Hoogsteen or Watson-Crick base pairing?
Q41268426	Accommodation of profound sequence differences at the interfaces of eubacterial RNA polymerase multi-protein assembly
Q24793849	Accuracy of structure-derived properties in simple comparative models of protein structures
Q31037390	Accurate and efficient loop selections by the DFIRE-based all-atom statistical potential.
Q37253674	Accurate prediction of the bound form of the Akt pleckstrin homology domain using normal mode analysis to explore structural flexibility
Q46863803	Acetylcholine nicotinic receptors: finding the putative binding site of allosteric modulators using the "blind docking" approach
Q30395939	Achievements and Challenges in Computational Protein Design
Q45306902	Active site prediction for comparative model structures with thematics
Q41438539	Acyl-2-aminobenzimidazoles: a novel class of neuroprotective agents targeting mGluR5
Q90173095	Adaption of human antibody λ and κ light chain architectures to CDR repertoires
Q28082537	Advancements in therapeutically targeting orphan GPCRs
Q22241408	Advances in Homology Protein Structure Modeling
Q35840288	Aggregate reactivation mediated by the Hsp100 chaperones
Q30408373	All-atom modeling of anisotropic atomic fluctuations in protein crystal structures
Q38387054	Allosteric Dynamic Control of Binding.
Q36490217	Allosteric Inhibition of Human Ribonucleotide Reductase by dATP Entails the Stabilization of a Hexamer.
Q83227485	Allosteric activation of the nitric oxide receptor soluble guanylate cyclase mapped by cryo-electron microscopy
Q34620088	Allosteric antagonist binding sites in class B GPCRs: corticotropin receptor 1.
Q34395251	Allosteric communication across the native and mutated KIT receptor tyrosine kinase
Q47567087	Allosteric control of antibody-prion recognition through oxidation of a disulfide bond between the CH and CL chains
Q41609096	Allosteric control of kinesin's motor domain by tubulin: a molecular dynamics study
Q37608491	Allosteric modulation of a cannabinoid G protein-coupled receptor: binding site elucidation and relationship to G protein signaling
Q60309406	Amino acid residues in five separate HLA genes can explain most of the known associations between the MHC and primary biliary cholangitis
Q98782068	An Aryl Hydrocarbon Receptor from the Caecilian Gymnopis multiplicata Suggests Low Dioxin Affinity in the Ancestor of All Three Amphibian Orders
Q35679706	An Aryl Hydrocarbon Receptor from the Salamander Ambystoma mexicanum Exhibits Low Sensitivity to 2,3,7,8-Tetrachlorodibenzo-p-dioxin
Q30374826	An Improved Integration of Template-Based and Template-Free Protein Structure Modeling Methods and its Assessment in CASP11
Q31148716	An allosteric signaling pathway of human 3-phosphoglycerate kinase from force distribution analysis
Q60045400	An improved protein structure evaluation using a semi-empirically derived structure property
Q34962635	An in silico analysis of troponin I mutations in hypertrophic cardiomyopathy of Indian origin
Q35915063	An integrated in silico approach for functional and structural impact of non- synonymous SNPs in the MYH1 gene in Jeju Native Pigs
Q38089807	An overview of recent developments in GPCR modelling: methods and validation
Q41984897	An unconventional copper protein required for cytochrome c oxidase respiratory function under extreme acidic conditions
Q33281855	Analysis of murine hepatitis virus strain A59 temperature-sensitive mutant TS-LA6 suggests that nsp10 plays a critical role in polyprotein processing
Q58756307	Analyzing protein topology based on Laguerre tessellation of a pore-traversing water network
Q83230306	Ancestral reconstruction reveals mechanisms of ERK regulatory evolution
Q46849544	Anti-HIV cyclotides from the Chinese medicinal herb Viola yedoensis.
Q52944266	Anti-angiogenic activity of PSA-derived peptides.
Q41172450	Antibodies as a model system for comparative model refinement.
Q30398990	Antibody H3 Structure Prediction
Q47571305	Antibody modeling using the prediction of immunoglobulin structure (PIGS) web server [corrected].
Q30360105	Antibody structure determination using a combination of homology modeling, energy-based refinement, and loop prediction.
Q40129849	Antileishmanial activity and tubulin polymerization inhibition of podophyllotoxin derivatives on Leishmania infantum
Q35782062	Antisera Against Certain Conserved Surface-Exposed Peptides of Nontypeable Haemophilus influenzae Are Protective.
Q27666848	Applying Molecular Dynamics Simulations to Identify Rarely Sampled Ligand-bound Conformational States of Undecaprenyl Pyrophosphate Synthase, an Antibacterial Target
Q40403023	ArchDB: automated protein loop classification as a tool for structural genomics.
Q43207285	Archaea recruited D-Tyr-tRNATyr deacylase for editing in Thr-tRNA synthetase
Q27696307	Architecture and conformational switch mechanism of the ryanodine receptor
Q59808041	Architecture and subunit arrangement of the complete Saccharomyces cerevisiae COMPASS complex
Q46008443	Architecture of the type IV coupling protein complex of Legionella pneumophila.
Q41870856	Assessing protein loop flexibility by hierarchical Monte Carlo sampling
Q28534461	Assessment and challenges of ligand docking into comparative models of G-protein coupled receptors
Q30409206	Assessment of protein structure refinement in CASP9.
Q30380207	Assessment of the protein-structure refinement category in CASP8
Q41843852	Assignment of pterin deaminase activity to an enzyme of unknown function guided by homology modeling and docking
Q83225728	Asymmetrical diversification of the receptor-ligand interaction controlling self-incompatibility in Arabidopsis
Q30355358	Atomic-accuracy prediction of protein loop structures through an RNA-inspired Ansatz.
Q34010366	Atomistic insights into regulatory mechanisms of the HER2 tyrosine kinase domain: a molecular dynamics study
Q54294766	Atomistic insights into the lung cancer-associated L755P mutation in HER2 resistance to lapatinib: a molecular dynamics study.
Q36518348	Autoinhibitory Interdomain Interactions and Subfamily-specific Extensions Redefine the Catalytic Core of the Human DEAD-box Protein DDX3.
Q30361881	Automated Aufbau of antibody structures from given sequences using Macromoltek's SmrtMolAntibody.
Q64067249	Automated cryo-EM structure refinement using correlation-driven molecular dynamics
Q30341674	Automated protein structure homology modeling: a progress report.
Q30341442	Automated structure prediction of weakly homologous proteins on a genomic scale
Q35818943	Automatic Prediction of Protein 3D Structures by Probabilistic Multi-template Homology Modeling
Q41918173	Autosomal dominant transmission of complicated hereditary spastic paraplegia due to a dominant negative mutation of KIF1A, SPG30 gene.
Q34374455	AvrRpm1 missense mutations weakly activate RPS2-mediated immune response in Arabidopsis thaliana
Q44373387	BRCA1 point mutations in premenopausal breast cancer patients from Central Sudan.
Q28117008	Bifunctional homodimeric triokinase/FMN cyclase: contribution of protein domains to the activities of the human enzyme and molecular dynamics simulation of domain movements
Q33822757	Binding of small molecules to cavity forming mutants of a de novo designed protein
Q83973804	Binding site characterization of G protein-coupled receptor by alanine-scanning mutagenesis using molecular dynamics and binding free energy approach: application to C-C chemokine receptor-2 (CCR2)
Q46850853	Biochemical analysis and kinetic modeling of the thermal inactivation of MBP-fused heparinase I: implications for a comprehensive thermostabilization strategy
Q28221288	CD3 delta establishes a functional link between the T cell receptor and CD8
Q34085563	CHARMM additive all-atom force field for carbohydrate derivatives and its utility in polysaccharide and carbohydrate-protein modeling.
Q24611955	CIPRO 2.5: Ciona intestinalis protein database, a unique integrated repository of large-scale omics data, bioinformatic analyses and curated annotation, with user rating and reviewing functionality
Q90613746	Cellular Processing of the ABCG2 Transporter-Potential Effects on Gout and Drug Metabolism
Q49461101	Ceratocystis cacaofunesta genome analysis reveals a large expansion of extracellular phosphatidylinositol-specific phospholipase-C genes (PI-PLC).
Q55344910	Chaperna-Mediated Assembly of Ferritin-Based Middle East Respiratory Syndrome-Coronavirus Nanoparticles.
Q44016911	Characterization of a hyperthermophilic P-type ATPase from Methanococcus jannaschii expressed in yeast
Q53437158	Characterization of adenosine receptor in its native environment: insights from molecular dynamics simulations of palmitoylated/glycosylated, membrane-integrated human A(2B) adenosine receptor.
Q64120431	Characterization of cancer-associated IDH2 mutations that differ in tumorigenicity, chemosensitivity and 2-hydroxyglutarate production
Q28472105	Characterization of the Entamoeba histolytica ornithine decarboxylase-like enzyme
Q38077229	Characterization of the dynamic events of GPCRs by automated computational simulations
Q39131216	Characterization of the infectious salmon anemia virus fusion protein
Q26779035	Charting a Path to Success in Virtual Screening
Q33584492	Cheminformatics-aided discovery of small-molecule Protein-Protein Interaction (PPI) dual inhibitors of Tumor Necrosis Factor (TNF) and Receptor Activator of NF-κB Ligand (RANKL).
Q33449492	Closing the side-chain gap in protein loop modeling
Q30380766	Clustering and percolation in protein loop structures.
Q28544906	Co-conserved MAPK features couple D-domain docking groove to distal allosteric sites via the C-terminal flanking tail
Q28552871	Coenzyme Q Biosynthesis: Evidence for a Substrate Access Channel in the FAD-Dependent Monooxygenase Coq6
Q41642027	Combined computational and experimental analysis of a complex of ribonuclease III and the regulatory macrodomain protein, YmdB
Q91111834	Communication between the Ligand-Binding Pocket and the Activation Function-2 Domain of Androgen Receptor Revealed by Molecular Dynamics Simulations
Q30366550	Comparative Protein Structure Modeling Using MODELLER
Q41144462	Comparative Protein Structure Modeling Using MODELLER.
Q46629154	Comparative Protein Structure Modeling Using MODELLER.
Q58043842	Comparative Protein Structure Modeling and its Applications to Drug Discovery
Q36599268	Comparative analysis of homology models of the AH receptor ligand binding domain: verification of structure-function predictions by site-directed mutagenesis of a nonfunctional receptor
Q46478182	Comparative analysis of receptor binding by chicken and human interleukin-1β.
Q24811118	Comparative modelling of protein structure and its impact on microbial cell factories
Q34431019	Comparative molecular modeling study of Arabidopsis NADPH-dependent thioredoxin reductase and its hybrid protein
Q29615142	Comparative protein structure modeling using Modeller
Q64124737	Comparison of Alicyclobacillus acidocaldarius o-Succinylbenzoate Synthase to Its Promiscuous N-Succinylamino Acid Racemase/ o-Succinylbenzoate Synthase Relatives
Q36095703	Comparison of SARS and NL63 papain-like protease binding sites and binding site dynamics: inhibitor design implications
Q47335662	Comparison of molecular dynamics averaged structures for complexes of normal and oncogenic ras-p21 with SOS nucleotide exchange protein, containing computed conformations for three crystallographically undefined domains, suggests a potential role of
Q30372639	Complete atomistic model of a bacterial cytoplasm for integrating physics, biochemistry, and systems biology.
Q27472918	Complete predicted three-dimensional structure of the facilitator transmembrane protein and hepatitis C virus receptor CD81: conserved and variable structural domains in the tetraspanin superfamily
Q36251118	Computational Analysis of Residue Interaction Networks and Coevolutionary Relationships in the Hsp70 Chaperones: A Community-Hopping Model of Allosteric Regulation and Communication
Q93080951	Computational Drug Repurposing Algorithm Targeting TRPA1 Calcium Channel as a Potential Therapeutic Solution for Multiple Sclerosis
Q47362549	Computational Modeling of the Hsp90 Interactions with Cochaperones and Small-Molecule Inhibitors
Q33901743	Computational and Experimental Characterization of Patient Derived Mutations Reveal an Unusual Mode of Regulatory Spine Assembly and Drug Sensitivity in EGFR Kinase.
Q39884397	Computational characterization of how the VX nerve agent binds human serum paraoxonase 1.
Q64103844	Computational design of structured loops for new protein functions
Q35594835	Computational methods in drug design: modeling G protein-coupled receptor monomers, dimers, and oligomers
Q44111505	Computational model of the HIV-1 subtype A V3 loop: study on the conformational mobility for structure-based anti-AIDS drug design
Q30363516	Computational modeling of allosteric regulation in the hsp90 chaperones: a statistical ensemble analysis of protein structure networks and allosteric communications.
Q28821078	Computational modeling of laminin N-terminal domains using sparse distance constraints from disulfide bonds and chemical cross-linking
Q30374663	Computational modeling of structurally conserved cancer mutations in the RET and MET kinases: the impact on protein structure, dynamics, and stability.
Q30406999	Computational protein design to reengineer stromal cell-derived factor-1α generates an effective and translatable angiogenic polypeptide analog
Q91525393	Computational screening of nanoparticles coupling to Aβ40 peptides and fibrils
Q45741706	Computational study and peptide inhibitors design for the CDK9 - cyclin T1 complex
Q90044975	Computational study of paroxetine-like inhibitors reveals new molecular insight to inhibit GRK2 with selectivity over ROCK1
Q57896855	Conformational Dynamics of Herpesviral NEC Proteins in Different Oligomerization States
Q42318784	Conformational changes during human P2X7 receptor activation examined by structural modelling and cysteine-based cross-linking studies
Q35034161	Conformational changes in talin on binding to anionic phospholipid membranes facilitate signaling by integrin transmembrane helices
Q34972050	Conformational changes in the lower palm domain of ASIC1a contribute to desensitization and RFamide modulation
Q38659159	Conformational preludes to the latency transition in PAI-1 as determined by atomistic computer simulations and hydrogen/deuterium-exchange mass spectrometry.
Q28547096	Conformational sampling and structure prediction of multiple interacting loops in soluble and β-barrel membrane proteins using multi-loop distance-guided chain-growth Monte Carlo method
Q38201039	Conformational sampling in template-free protein loop structure modeling: an overview
Q57077666	Conformational selection through electrostatics: Free energy simulations of gtp and gdp binding to archaeal initiation factor 2
Q27654522	Contraction of the disordered loop located within C-terminal domain of the transcriptional regulator HlyIIR causes its structural rearrangement
Q36471188	Correlation of chemical shifts predicted by molecular dynamics simulations for partially disordered proteins
Q27331720	Corresponding functional dynamics across the Hsp90 Chaperone family: insights from a multiscale analysis of MD simulations
Q50047445	Coupled regulation by the juxtamembrane and sterile α motif (SAM) linker is a hallmark of Ephrin tyrosine kinase evolution.
Q50936574	Cross-talk between the ligand- and DNA-binding domains of estrogen receptor.
Q37563536	Crucial positively charged residues for ligand activation of the GPR35 receptor
Q27673796	Crystal Structure of C-terminal Truncated Apolipoprotein A-I Reveals the Assembly of High Density Lipoprotein (HDL) by Dimerization
Q24602248	Crystal structure of human beta-hexosaminidase B: understanding the molecular basis of Sandhoff and Tay-Sachs disease
Q27674147	Crystal structure of nucleotide-free dynamin
Q36922857	Crystal structure of the C-terminal domain of the ɛ subunit of human translation initiation factor eIF2B.
Q27685230	Crystal structure of the yeast TSC1 core domain and implications for tuberous sclerosis pathological mutations
Q64113855	Current Advances in Studying Clinically Relevant Transporters of the Solute Carrier (SLC) Family by Connecting Computational Modeling and Data Science
Q36454443	CyBase: a database of cyclic protein sequences and structures, with applications in protein discovery and engineering
Q30332780	Cyclic coordinate descent: A robotics algorithm for protein loop closure.
Q42912721	Cysteines in the loop between IS5 and the pore helix of Ca(V)3.1 are essential for channel gating
Q38527937	DIRECT-ID: An automated method to identify and quantify conformational variations--application to β2 -adrenergic GPCR.
Q92202873	DaReUS-Loop: a web server to model multiple loops in homology models
Q58747305	DaReUS-Loop: accurate loop modeling using fragments from remote or unrelated proteins
Q35855961	Dancing through Life: Molecular Dynamics Simulations and Network-Centric Modeling of Allosteric Mechanisms in Hsp70 and Hsp110 Chaperone Proteins
Q59545957	De Novo Mutations in the Motor Domain of KIF1A Cause Cognitive Impairment, Spastic Paraparesis, Axonal Neuropathy, and Cerebellar Atrophy
Q28550223	Deciphering Dimerization Modes of PAS Domains: Computational and Experimental Analyses of the AhR:ARNT Complex Reveal New Insights Into the Mechanisms of AhR Transformation
Q35885592	Deciphering the mismatch recognition cycle in MutS and MSH2-MSH6 using normal-mode analysis
Q28260419	Defining the loop structures in proteins based on composite β-turn mimics
Q54368186	Definition of the binding mode of phosphoinositide 3-kinase α-selective inhibitor A-66S through molecular dynamics simulation.
Q27677231	Design of a binding scaffold based on variable lymphocyte receptors of jawless vertebrates by module engineering
Q38729630	Design, Synthesis, and Evaluation of Dasatinib-Amino Acid and Dasatinib-Fatty Acid Conjugates as Protein Tyrosine Kinase Inhibitors.
Q50017426	Design, Synthesis, and Evaluation of GLUT Inhibitors.
Q35236118	Design, syntheses, and pharmacological characterization of 17-cyclopropylmethyl-3,14β-dihydroxy-4,5α-epoxy-6α-(isoquinoline-3'-carboxamido)morphinan analogues as opioid receptor ligands
Q50985152	Designing the Sniper: Improving Targeted Human Cytolytic Fusion Proteins for Anti-Cancer Therapy via Molecular Simulation.
Q33808132	Detection of the TCDD binding-fingerprint within the Ah receptor ligand binding domain by structurally driven mutagenesis and functional analysis.
Q43238964	Determination of the active site of Sphingobium chlorophenolicum 2,6-dichlorohydroquinone dioxygenase (PcpA).
Q97539807	Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus
Q42109476	Development of a new physics-based internal coordinate mechanics force field and its application to protein loop modeling
Q35312332	Dietary isothiocyanate-induced apoptosis via thiol modification of DNA topoisomerase IIα.
Q33826885	Different potential of C-type lectin-mediated entry between Marburg virus strains
Q30353164	Differential modulation of functional dynamics and allosteric interactions in the Hsp90-cochaperone complexes with p23 and Aha1: a computational study.
Q35129029	Dihedral-angle information entropy as a gauge of secondary structure propensity
Q30370976	Dimerization and phosphatase activity of calcyclin-binding protein/Siah-1 interacting protein: the influence of oxidative stress.
Q42232452	Discerning intersecting fusion-activation pathways in the Nipah virus using machine learning
Q54968572	Discovery and Biochemical Characterization of PlyP56, PlyN74, and PlyTB40-Bacillus Specific Endolysins.
Q52668077	Discovery of benzothiazolylquinoline conjugates as novel human A3 receptor antagonists: biological evaluations and molecular docking studies.
Q30367066	Discovery of novel DUSP16 phosphatase inhibitors through virtual screening with homology modeled protein structure.
Q39292974	Discovery of novel vascular endothelial growth factor receptor 2 inhibitors: a virtual screening approach
Q37318387	Discovery, identification and comparative analysis of non-specific lipid transfer protein (nsLtp) family in Solanaceae
Q63987396	Dishevelled-3 conformation dynamics analyzed by FRET-based biosensors reveals a key role of casein kinase 1
Q48051459	Distance-Guided Forward and Backward Chain-Growth Monte Carlo Method for Conformational Sampling and Structural Prediction of Antibody CDR-H3 Loops
Q42694873	Distinct second extracellular loop structures of the brain cannabinoid CB(1) receptor: implication in ligand binding and receptor function
Q47097154	Diverse effects of distance cutoff and residue interval on the performance of distance-dependent atom-pair potential in protein structure prediction
Q24531477	Diversity and function of mutations in p450 oxidoreductase in patients with Antley-Bixler syndrome and disordered steroidogenesis
Q92647543	Diversity of oligomerization in Drosophila semaphorins suggests a mechanism of functional fine-tuning
Q36443377	DnaC traps DnaB as an open ring and remodels the domain that binds primase.
Q41710215	Docking analysis insights quercetin can be a non-antibiotic adjuvant by inhibiting Mmr drug efflux pump in Mycobacterium sp. and its homologue EmrE in Escherichia coli
Q27313291	Docking studies of Pakistani HCV NS3 helicase: a possible antiviral drug target
Q30379422	Docking studies of structurally diverse antimalarial drugs targeting PfATP6: no correlation between in silico binding affinity and in vitro antimalarial activity.
Q86169619	Docking-based three-dimensional quantitative structure-activity relationship (3D-QSAR) predicts binding affinities to aryl hydrocarbon receptor for polychlorinated dibenzodioxins, dibenzofurans, and biphenyls
Q36977345	Domain Movements upon Activation of Phenylalanine Hydroxylase Characterized by Crystallography and Chromatography-Coupled Small-Angle X-ray Scattering
Q36116699	Dominant transmission of de novo KIF1A motor domain variant underlying pure spastic paraplegia
Q34447486	Double domain swapping in bovine seminal RNase: formation of distinct N- and C-swapped tetramers and multimers with increasing biological activities
Q90429563	Drosophila OTK Is a Glycosaminoglycan-Binding Protein with High Conformational Flexibility
Q35963327	Dynamics of firefly luciferase inhibition by general anesthetics: Gaussian and anisotropic network analyses
Q44144522	EGF domain II of protein Pb28 from Plasmodium berghei interacts with monoclonal transmission blocking antibody 13.1.
Q33619364	ELIC-α7 Nicotinic acetylcholine receptor (α7nAChR) chimeras reveal a prominent role of the extracellular-transmembrane domain interface in allosteric modulation
Q33659530	EasyModeller: A graphical interface to MODELLER
Q37848236	Effect of the termini of RNase Hs from Chlamydophila pneumoniae on enzymatic biochemical characterization
Q30378114	Effective knowledge-based potentials
Q48063073	Effects from metal ion in tumor endothelial marker 8 and anthrax protective antigen: BioLayer Interferometry experiment and molecular dynamics simulation study
Q36267581	Effects of FGFR2 kinase activation loop dynamics on catalytic activity
Q47105500	Effects of Periplasmic Chaperones and Membrane Thickness on BamA-Catalyzed Outer-Membrane Protein Folding
Q37479619	Efficient algorithms to explore conformation spaces of flexible protein loops
Q42105485	Elimination of 2-keto-3-deoxy-D-glycero-D-galacto-nonulosonic acid 9-phosphate synthase activity from human N-acetylneuraminic acid 9-phosphate synthase by a single mutation
Q50538928	Elucidating Mechanisms of Molecular Recognition Between Human Argonaute and miRNA Using Computational Approaches.
Q36629045	Elucidation of relaxin-3 binding interactions in the extracellular loops of RXFP3.
Q30371845	Embedded cholesterol in the nicotinic acetylcholine receptor
Q30358225	Emerging Computational Methods for the Rational Discovery of Allosteric Drugs.
Q30152632	Engineering protein stability with atomic precision in a monomeric miniprotein.
Q94481764	Enhancing fragment-based protein structure prediction by customising fragment cardinality according to local secondary structure
Q53185257	Ensemble-Based Virtual Screening and Experimental Validation of Inhibitors Targeting a Novel Site of Human DNMT1.
Q36060332	Ensembler: Enabling High-Throughput Molecular Simulations at the Superfamily Scale
Q44470827	Enzymatic characterization and molecular modeling of an evolutionarily interesting fungal β-N-acetylhexosaminidase.
Q57014366	Essential Role of Hydration in Aggregation of Misfolded Prion Proteins: Quantification by Molecular Theory of Solvation
Q36958036	Estimation of ligand efficacies of metabotropic glutamate receptors from conformational forces obtained from molecular dynamics simulations.
Q34064011	Evaluating conformational free energies: the colony energy and its application to the problem of loop prediction
Q39864455	Evidence for phosphatase activity of p27SJ and its impact on the cell cycle.
Q45007494	Evolutionarily evolved discriminators in the 3-TPR domain of the Toc64 family involved in protein translocation at the outer membrane of chloroplasts and mitochondria
Q27662913	Exploiting Antigenic Diversity for Vaccine Design: THE CHLAMYDIA ArtJ PARADIGM
Q53348054	Exploration of the binding modes of L-asparaginase complexed with its amino acid substrates by molecular docking, dynamics and simulation.
Q35127184	Exploring a coarse-grained distributive strategy for finite-difference Poisson-Boltzmann calculations
Q34540970	Exploring binding properties of agonists interacting with a δ-opioid receptor
Q30364967	Exploring conformational space using a mean field technique with MOLS sampling.
Q35005457	Exploring molecular mechanisms of ligand recognition by opioid receptors with metadynamics
Q58743634	Exploring the Ligand Efficacy of Cannabinoid Receptor 1 (CB1) using Molecular Dynamics Simulations
Q41383381	Exploring the PDE5 H-pocket by ensemble docking and structure-based design and synthesis of novel β-carboline derivatives.
Q51317255	Exploring the energy landscapes of flexible molecular loops using higher-dimensional continuation.
Q41893871	Expression and properties of the highly alkalophilic phenylalanine ammonia-lyase of thermophilic Rubrobacter xylanophilus
Q37372651	Extensive conformational transitions are required to turn on ATP hydrolysis in myosin.
Q30371233	Extracellular domain alterations impact surface expression of stimulatory natural killer cell receptor KIR2DS5.
Q30400754	Fast de novo discovery of low-energy protein loop conformations.
Q58700891	Fast design of arbitrary length loops in proteins using InteractiveRosetta
Q35156988	Fast protein loop sampling and structure prediction using distance-guided sequential chain-growth Monte Carlo method
Q35098071	Five checkpoints maintaining the fidelity of transcription by RNA polymerases in structural and energetic details
Q36365102	Flexible connection of the N-terminal domain in ClpB modulates substrate binding and the aggregate reactivation efficiency
Q27681045	Formylglycinamide ribonucleotide amidotransferase from Salmonella typhimurium: role of ATP complexation and the glutaminase domain in catalytic coupling
Q35529563	Fragment based group QSAR and molecular dynamics mechanistic studies on arylthioindole derivatives targeting the α-β interfacial site of human tubulin
Q39434682	Fragment-based modeling of membrane protein loops: successes, failures, and prospects for the future
Q37050678	Functional Characterization of Soybean Glyma04g39610 as a Brassinosteroid Receptor Gene and Evolutionary Analysis of Soybean Brassinosteroid Receptors.
Q40949543	Functional analysis of a structural model of the ATP-binding site of the KATP channel Kir6.2 subunit.
Q104471870	Functional and computational identification of a rescue mutation near the active site of an mRNA methyltransferase
Q36870576	Functional interplay between NTP leaving group and base pair recognition during RNA polymerase II nucleotide incorporation revealed by methylene substitution
Q27323329	GPCR-ModSim: A comprehensive web based solution for modeling G-protein coupled receptors
Q89658357	GPR6 Structural Insights: Homology Model Construction and Docking Studies
Q56532488	Gating mechanisms during actin filament elongation by formins
Q37283552	Generation of a flexible loop structural ensemble and its application to induced-fit structural changes following ligand binding
Q36138901	Genome-wide survey and phylogeny of S-Ribosylhomocysteinase (LuxS) enzyme in bacterial genomes.
Q34776476	Ginsenosides are novel naturally-occurring aryl hydrocarbon receptor ligands
Q58751660	Glucosylceramide modifies the LPS-induced inflammatory response in macrophages and the orientation of the LPS/TLR4 complex in silico
Q36588528	HIV coreceptor tropism determination and mutational pattern identification
Q41527488	HSP70-Hrd1 axis precludes the oncorepressor potential of N-terminal misfolded Blimp-1s in lymphoma cells
Q52307551	HU-446 and HU-465, Derivatives of the Non-psychoactive Cannabinoid Cannabidiol, Decrease the Activation of Encephalitogenic T Cells.
Q33772568	Heat Capacity Changes for Transition-State Analogue Binding and Catalysis with Human 5'-Methylthioadenosine Phosphorylase.
Q33614589	Heterotypic humoral and cellular immune responses following Norwalk virus infection
Q30157152	Hierarchical modeling of activation mechanisms in the ABL and EGFR kinase domains: thermodynamic and mechanistic catalysts of kinase activation by cancer mutations
Q36911443	High Level Secretion of Laccase (LccH) from a Newly Isolated White-Rot Basidiomycete, Hexagonia hirta MSF2.
Q35929274	Highly conserved regions in Ebola virus RNA dependent RNA polymerase may be act as a universal novel peptide vaccine target: a computational approach
Q39831076	Homology modeling and docking studies of human Bcl-2L10 protein
Q34188857	Homology modeling and molecular dynamics simulations of transmembrane domain structure of human neuronal nicotinic acetylcholine receptor
Q41912128	Homology modeling and virtual screening studies of FGF-7 protein-a structure-based approach to design new molecules against tumor angiogenesis
Q34951906	Homology modeling of Ferredoxin-nitrite reductase from Arabidopsis thaliana
Q43241599	Homology modeling of Mycobacterium tuberculosis 2C-methyl-D-erythritol-4-phosphate cytidylyltransferase, the third enzyme in the MEP pathway for isoprenoid biosynthesis.
Q37420190	Homology modeling of human Toll-like receptors TLR7, 8, and 9 ligand-binding domains
Q34651393	Homology modeling of opioid receptor-ligand complexes using experimental constraints
Q84417497	Homology modeling of the structure of acyl coA:isopenicillin N-acyltransferase (IAT) from Penicillium chrysogenum. IAT interaction studies with isopenicillin-N, combining molecular dynamics simulations and docking
Q24674821	Homology modeling using parametric alignment ensemble generation with consensus and energy-based model selection
Q45232745	Homology modeling, force field design, and free energy simulation studies to optimize the activities of histone deacetylase inhibitors
Q47797032	Homology modelling and molecular dynamics simulations: comparative studies of human aquaporin-1.
Q37431590	Homology modelling: a review about the method on hand of the diabetic antigen GAD 65 structure prediction
Q28541374	Hotspot mutations in KIT receptor differentially modulate its allosterically coupled conformational dynamics: impact on activation and drug sensitivity
Q35686986	How Co-translational Folding of Multi-domain Protein Is Affected by Elongation Schedule: Molecular Simulations
Q93058867	How Electrostatic Coupling Enables Conformational Plasticity in a Tyrosine Kinase
Q30430059	How long is a piece of loop?
Q61135820	How nanoscale protein interactions determine the mesoscale dynamic organisation of bacterial outer membrane proteins
Q30411400	How noise in force fields can affect the structural refinement of protein models?
Q30372425	How well can the accuracy of comparative protein structure models be predicted?
Q24801065	Human glutaminyl cyclase and bacterial zinc aminopeptidase share a common fold and active site
Q36957378	Hydration effects on the HET-s prion and amyloid-beta fibrillous aggregates, studied with three-dimensional molecular theory of solvation
Q36393085	ISAMBARD: an open-source computational environment for biomolecular analysis, modelling and design
Q47780253	Identification and characterization of ErbB4 kinase inhibitors for effective breast cancer therapy
Q42925719	Identification and characterization of a hitherto unknown nucleotide-binding domain and an intricate interdomain regulation in HflX-a ribosome binding GTPase
Q43636703	Identification and characterization of a protein-tyrosine phosphatase in Leishmania: Involvement in virulence
Q55392497	Identification of Peptide Antagonists to Thioredoxin Glutathione Reductase of Schistosoma japonicum.
Q64065266	Identification of a Novel Anti-cancer Protein, FIP-bbo, from Botryobasidium botryosum and Protein Structure Analysis using Molecular Dynamic Simulation
Q37519411	Identification of a novel binding site between HIV type 1 Nef C-terminal flexible loop and AP2 required for Nef-mediated CD4 downregulation
Q64097123	Identification of a novel potassium channel (GiK) as a potential drug target in : Computational descriptions of binding sites
Q28507975	Identification of crucial amino acids in mouse aldehyde oxidase 3 that determine substrate specificity
Q37042152	Identification of human immunodeficiency virus type 1 (HIV-1) gp120-binding sites on scavenger receptor cysteine rich 1 (SRCR1) domain of gp340.
Q40495564	Identification of internalin-A-like virulent proteins in Leishmania donovani
Q34698788	Identification of local conformational similarity in structurally variable regions of homologous proteins using protein blocks
Q48048743	Identification of novel inhibitors of the translationally controlled tumor protein (TCTP): insights from molecular dynamics
Q42006954	Identification of regions critically affecting kinetics and allosteric regulation of the Escherichia coli ADP-glucose pyrophosphorylase by modeling and pentapeptide-scanning mutagenesis
Q33887246	Identification of the GPR55 agonist binding site using a novel set of high-potency GPR55 selective ligands
Q29871509	Identification of the active form of endothelial lipase, a homodimer in a head-to-tail conformation
Q24294422	Identification of zyklopen, a new member of the vertebrate multicopper ferroxidase family, and characterization in rodents and human cells
Q92523951	Identifying the molecular target sites for CFTR potentiators GLPG1837 and VX-770
Q33636152	Improving predicted protein loop structure ranking using a Pareto-optimality consensus method
Q90212285	In Silico Methods in Antibody Design
Q35934088	In Silico Modeling of Novel Drug Ligands for Treatment of Concussion Associated Tauopathy
Q41440894	In Silico Structural and Functional Annotation of Hypothetical Proteins of Vibrio cholerae O139.
Q55114838	In silico assessment of the conduction mechanism of the Ryanodine Receptor 1 reveals previously unknown exit pathways.
Q36355727	In silico biology of H1N1: molecular modelling of novel receptors and docking studies of inhibitors to reveal new insight in flu treatment.
Q37319169	In silico characterization and homology modeling of thylakoid-bound ascorbate peroxidase from a drought tolerant wheat cultivar.
Q41821713	In silico expressed sequence tag analysis in identification of probable diabetic genes as virtual therapeutic targets
Q35238167	In silico insights into protein-protein interactions and folding dynamics of the saposin-like domain of Solanum tuberosum aspartic protease
Q47790895	In silico interaction analysis of cannabinoid receptor interacting protein 1b (CRIP1b) - CB1 cannabinoid receptor
Q42175038	In silico model of DSF synthase RpfF protein from Xanthomonas oryzae pv. Oryzae: a novel target for bacterial blight of rice disease
Q41243043	In silico model of the human ClC-Kb chloride channel: pore mapping, biostructural pathology and drug screening
Q30491595	In silico models for the human alpha4beta2 nicotinic acetylcholine receptor
Q47844404	In silico probing and biological evaluation of SETDB1/ESET-targeted novel compounds that reduce tri-methylated histone H3K9 (H3K9me3) level
Q43594206	In silico protein recombination: enhancing template and sequence alignment selection for comparative protein modelling
Q43233994	In silico studies of C 3 metabolic pathway proteins of wheat (Triticum aestivum).
Q27679340	In situ structural analysis of the Yersinia enterocolitica injectisome
Q34504744	In the multi-domain protein adenylate kinase, domain insertion facilitates cooperative folding while accommodating function at domain interfaces
Q42273342	In-silico structural and functional characterization of a V. cholerae O395 hypothetical protein containing a PDZ1 and an uncommon protease domain
Q42959523	Including Functional Annotations and Extending the Collection of Structural Classifications of Protein Loops (ArchDB).
Q36753696	Influence of RNA Binding on the Structure and Dynamics of the Lassa Virus Nucleoprotein
Q30492256	Influence of local sequence context on damaged base conformation in human DNA polymerase iota: molecular dynamics studies of nucleotide incorporation opposite a benzo[a]pyrene-derived adenine lesion
Q33733606	Innate immune detection of the type III secretion apparatus through the NLRC4 inflammasome
Q42268957	Insight into the structural stability of wild type and mutants of the tobacco etch virus protease with molecular dynamics simulations
Q28727426	Insight into the structure, dynamics and the unfolding property of amylosucrases: implications of rational engineering on thermostability
Q42002958	Insights from the molecular characterization of mercury stress proteins identified by proteomics in E.coli nissle 1917
Q34963583	Insights into the mechanism of pore opening of acid-sensing ion channel 1a.
Q57990921	Insights into the structural determinants of substrate specificity and activity in mouse aldehyde oxidases
Q84316043	Insilico Alpha-Helical Structural Recognition of Temporin Antimicrobial Peptides and Its Interactions with Middle East Respiratory Syndrome-Coronavirus
Q26777650	Integrative Modeling of Macromolecular Assemblies from Low to Near-Atomic Resolution
Q43242895	Interaction between the C termini of Alg13 and Alg14 mediates formation of the active UDP-N-acetylglucosamine transferase complex
Q92015544	Interactions between Yersinia pestis V-antigen (LcrV) and human Toll-like receptor 2 (TLR2) in a modelled protein complex and potential mechanistic insights
Q35004622	Interactions of the melanocortin-4 receptor with the peptide agonist NDP-MSH.
Q39511364	Interdomain Conformational Changes Provide Allosteric Regulation En Route To Chorismate
Q33685234	Internal proton transfer in the external pyridoxal 5'-phosphate Schiff base in dopa decarboxylase
Q47132843	Investigating Small-Molecule Ligand Binding to G Protein-Coupled Receptors with Biased or Unbiased Molecular Dynamics Simulations
Q48567170	Investigating the putative binding-mode of GABA and diazepam within GABA A receptor using molecular modeling.
Q41646833	Investigation of the dynamics of the viral immediate-early protein 1 in different conformations and oligomerization states
Q46314466	Ion channel gates: comparative analysis of energy barriers.
Q58708261	K binding and proton redistribution in the EP state of the H, K-ATPase
Q33955023	Key amino acid residues of ankyrin-sensitive phosphatidylethanolamine/phosphatidylcholine-lipid binding site of βI-spectrin.
Q27336481	Key diffusion mechanisms involved in regulating bidirectional water permeation across E. coli outer membrane lectin
Q52013586	Key issues in the computational simulation of GPCR function: representation of loop domains.
Q24632373	Kinetic and molecular analysis of 5-epiaristolochene 1,3-dihydroxylase, a cytochrome P450 enzyme catalyzing successive hydroxylations of sesquiterpenes
Q42032109	Kinetic properties and small-molecule inhibition of human myosin-6.
Q30356679	LEAP: highly accurate prediction of protein loop conformations by integrating coarse-grained sampling and optimized energy scores with all-atom refinement of backbone and side chains
Q92146694	LF4/MOK and a CDK-related kinase regulate the number and length of cilia in Tetrahymena
Q21256413	LRRML: a conformational database and an XML description of leucine-rich repeats (LRRs)
Q34387670	Lactisole interacts with the transmembrane domains of human T1R3 to inhibit sweet taste.
Q51602853	Large loop conformation sampling using the activation relaxation technique, ART-nouveau method.
Q90561582	Large-scale, dynamin-like motions of the human guanylate binding protein 1 revealed by multi-resolution simulations
Q36855635	Lesion specificity in the base excision repair enzyme hNeil1: modeling and dynamics studies
Q28552181	Ligand Docking to Intermediate and Close-To-Bound Conformers Generated by an Elastic Network Model Based Algorithm for Highly Flexible Proteins
Q42633034	Ligand binding to the voltage-gated Kv1.5 potassium channel in the open state--docking and computer simulations of a homology model
Q59489014	Ligand-, structure- and pharmacophore-based molecular fingerprints: a case study on adenosine A1, A2A, A2B, and A3 receptor antagonists
Q41677960	Ligand-induced allostery in the interaction of the Pseudomonas aeruginosa heme binding protein with heme oxygenase
Q52371594	Ligand-induced perturbation of the HIF-2α:ARNT dimer dynamics.
Q47396241	Ligand-supported Homology Modelling of Protein Binding-sites using Knowledge-based Potentials
Q34490693	Limits of ligand selectivity from docking to models: in silico screening for A(1) adenosine receptor antagonists
Q47650751	Lipids Shape the Electron Acceptor-Binding Site of the Peripheral Membrane Protein Dihydroorotate Dehydrogenase.
Q45310575	Localization of the N-terminal domain in light-harvesting chlorophyll a/b protein by EPR measurements
Q45125293	Loop flexibility and solvent dynamics as determinants for the selective inhibition of cyclin-dependent kinase 4: comparative molecular dynamics simulation studies of CDK2 and CDK4.
Q41875634	Loop modeling: Sampling, filtering, and scoring
Q29048209	LoopIng: a template-based tool for predicting the structure of protein loops
Q30427855	LoopWeaver: loop modeling by the weighted scaling of verified proteins
Q41809365	Loopholes and missing links in protein modeling
Q90045309	MARK4 protein can explore the active-like conformations in its non-phosphorylated state
Q64103570	MAW point mutation impairs H. Seropedicae RecA ATP hydrolysis and DNA repair without inducing large conformational changes in its structure
Q46459379	MHC Class II Risk Alleles and Amino Acid Residues in Idiopathic Membranous Nephropathy
Q39310404	MOLS sampling and its applications in structural biophysics
Q30382728	MUFOLD: A new solution for protein 3D structure prediction
Q45349630	Macrodomain-containing proteins are new mono-ADP-ribosylhydrolases.
Q56000942	Mapping Putative B-Cell Zika Virus NS1 Epitopes Provides Molecular Basis for Anti-NS1 Antibody Discrimination between Zika and Dengue Viruses
Q35804502	Mapping early conformational changes in alphaIIb and beta3 during biogenesis reveals a potential mechanism for alphaIIbbeta3 adopting its bent conformation
Q40704399	Mapping of interaction sites of the Schizosaccharomyces pombe protein Translin with nucleic acids and proteins: a combined molecular genetics and bioinformatics study
Q33820930	Mapping spatial relationships between residues in the ligand-binding domain of the 5-HT3 receptor using a molecular ruler
Q42391806	Mapping the catechol binding site in dopamine D₁ receptors: synthesis and evaluation of two parallel series of bicyclic dopamine analogues
Q35693509	Markov State Models Reveal a Two-Step Mechanism of miRNA Loading into the Human Argonaute Protein: Selective Binding followed by Structural Re-arrangement
Q50967058	MaxMod: a hidden Markov model based novel interface to MODELLER for improved prediction of protein 3D models.
Q89219274	Mechanical transduction of cytoplasmic-to-transmembrane-domain movements in a hyperpolarization-activated cyclic nucleotide-gated cation channel
Q27677451	Mechanism for priming DNA synthesis by yeast DNA Polymerase α
Q91940547	Mechanism of Sulfate Activation Catalyzed by ATP Sulfurylase - Magnesium Inhibits the Activity
Q37137479	Mechanism of artemisinin resistance for malaria PfATP6 L263 mutations and discovering potential antimalarials: An integrated computational approach.
Q39758058	Mechanisms for Two-Step Proton Transfer Reactions in the Outward-Facing Form of MATE Transporter.
Q28472177	Mechanisms of GII.4 norovirus persistence in human populations
Q51742381	Mechanistic Insights into R776H Mediated Activation of Epidermal Growth Factor Receptor Kinase.
Q40571401	Mechanistic insights from a refined three-dimensional model of integrin alphaIIbbeta3.
Q33990281	Mechanistic insights into xenon inhibition of NMDA receptors from MD simulations
Q28469135	Mechanochemical coupling in the myosin motor domain. I. Insights from equilibrium active-site simulations
Q88732468	Membrane fluctuations and acidosis regulate cooperative binding of 'marker of self' protein CD47 with the macrophage checkpoint receptor SIRPα
Q51239957	Metal ion site engineering indicates a global toggle switch model for seven-transmembrane receptor activation.
Q48020126	Methods for the Development of In Silico GPCR Models
Q33814436	Methylation of sulfhydryl groups: a new function for a family of small molecule plant O-methyltransferases
Q34316309	Mice lacking FABP9/PERF15 develop sperm head abnormalities but are fertile
Q51318577	Microscopic mechanisms that govern the titration response and pKa values of buried residues in staphylococcal nuclease mutants.
Q90153550	Microsecond Simulation of the Proteoglycan-like Region of Carbonic Anhydrase IX and Design of Chemical Inhibitors Targeting pH Homeostasis in Cancer Cells
Q52590223	Microtubule assembly governed by tubulin allosteric gain in flexibility and lattice induced fit.
Q21092257	Model structure of human APOBEC3G
Q58046189	Modeling Loops in Protein Structures
Q58449165	Modeling Structures and Motions of Loops in Protein Molecules
Q51891051	Modeling dimerizations of transmembrane proteins using Brownian dynamics simulations.
Q34352345	Modeling flexible loops in the dark-adapted and activated states of rhodopsin, a prototypical G-protein-coupled receptor
Q24598781	Modeling large regions in proteins: applications to loops, termini, and folding
Q41790490	Modeling mutations in protein structures
Q83450537	Modeling of the structure and interactions of the B. anthracis antitoxin, MoxX: deletion mutant studies highlight its modular structure and repressor function
Q34727938	Modeling proteins using a super-secondary structure library and NMR chemical shift information
Q27335863	Modeling signal propagation mechanisms and ligand-based conformational dynamics of the Hsp90 molecular chaperone full-length dimer
Q92134598	Modeling the binding of diverse ligands within the Ah receptor ligand binding domain
Q45535794	Modeling the helicase domain of Brome mosaic virus 1a replicase
Q35284220	Modeling, molecular dynamics, and docking assessment of transcription factor rho: a potential drug target in Brucella melitensis 16M.
Q28236254	Modeller: generation and refinement of homology-based protein structure models
Q34237113	Models to Approximate the Motions of Protein Loops
Q36824558	Modular aspects of kinesin force generation machinery
Q36044519	Molecular Basis of the Membrane Interaction of the β2e Subunit of Voltage-Gated Ca(2+) Channels
Q28548366	Molecular Determinants Underlying Binding Specificities of the ABL Kinase Inhibitors: Combining Alanine Scanning of Binding Hot Spots with Network Analysis of Residue Interactions and Coevolution
Q36065303	Molecular Dynamics Approach in the Comparison of Wild-Type and Mutant Paraoxonase-1 Apoenzyme Form
Q50790141	Molecular Dynamics Simulations to Investigate the Binding Mode of the Natural Product Liphagal with Phosphoinositide 3-Kinase α.
Q36291814	Molecular Modeling and Docking Study to Elucidate Novel Chikungunya Virus nsP2 Protease Inhibitors
Q47362097	Molecular Modeling of Multidrug Properties of Resistance Nodulation Division (RND) Transporters.
Q51603697	Molecular Modelling of G Protein-Coupled Receptors Through the Web.
Q90484517	Molecular Simulation of Oncostatin M and Receptor (OSM-OSMR) Interaction as a Potential Therapeutic Target for Inflammatory Bowel Disease
Q35781187	Molecular analysis of TCR and peptide/MHC interaction using P18-I10-derived peptides with a single D-amino acid substitution
Q37018242	Molecular and structural insight into lysine selection on substrate and ubiquitin lysine 48 by the ubiquitin-conjugating enzyme Cdc34
Q50075838	Molecular architecture of the glucose 1-phosphate site in ADP-glucose pyrophosphorylases.
Q30156098	Molecular basis for the structural stability of an enclosed β-barrel loop
Q55003590	Molecular details of dimerization kinetics reveal negligible populations of transient µ-opioid receptor homodimers at physiological concentrations.
Q41899831	Molecular details of the activation of the μ opioid receptor.
Q30391310	Molecular dynamics simulations and modelling of the residue interaction networks in the BRAF kinase complexes with small molecule inhibitors: probing the allosteric effects of ligand-induced kinase dimerization and paradoxical activation.
Q30159550	Molecular dynamics simulations of a bacterial autotransporter: NalP from Neisseria meningitidis.
Q35099468	Molecular dynamics simulations of the cardiac troponin complex performed with FRET distances as restraints
Q28542663	Molecular insights into the dynamics of pharmacogenetically important N-terminal variants of the human β2-adrenergic receptor
Q46441615	Molecular mechanism of oxidative stress perception by the Orp1 protein
Q40231350	Molecular mechanisms associated with Fluconazole resistance in clinical Candida albicans isolates from India
Q47566833	Molecular mechanisms underlying deoxy-ADP.Pi activation of pre-powerstroke myosin
Q43537068	Molecular modeling of the interleukin-19 receptor complex. Novel aspects of receptor recognition in the interleukin-10 cytokine family
Q55033575	Molecular modeling studies on series of Btk inhibitors using docking, structure-based 3D-QSAR and molecular dynamics simulation: a combined approach.
Q39015639	Molecular modeling, quantum polarized ligand docking and structure-based 3D-QSAR analysis of the imidazole series as dual AT(1) and ET(A) receptor antagonists.
Q30329498	Molecular modelling in structural biology.
Q41617618	Monte Carlo loop refinement and virtual screening of the thyroid-stimulating hormone receptor transmembrane domain
Q87058164	Multi-Dimensional Scaling and MODELLER-Based Evolutionary Algorithms for Protein Model Refinement
Q43214837	Multiscale Monte Carlo Sampling of Protein Sidechains: Application to Binding Pocket Flexibility
Q35857149	Murine hepatitis virus replicase protein nsp10 is a critical regulator of viral RNA synthesis
Q28741281	Mutant alcohol dehydrogenase leads to improved ethanol tolerance in Clostridium thermocellum
Q51032509	Mutantelec: An In Silico mutation simulation platform for comparative electrostatic potential profiling of proteins.
Q28478611	Mutation D816V alters the internal structure and dynamics of c-KIT receptor cytoplasmic region: implications for dimerization and activation mechanisms
Q42230320	Mutations in herpes simplex virus gD protein affect receptor binding by different molecular mechanisms
Q28236802	Mutations in the pleckstrin homology domain of dynamin 2 cause dominant intermediate Charcot-Marie-Tooth disease
Q63681670	Myoglobinopathy is an adult-onset autosomal dominant myopathy with characteristic sarcoplasmic inclusions
Q38673283	NADH oxidase activity of indoleamine 2,3-dioxygenase
Q27676088	NMR structure and dynamics of a designed water-soluble transmembrane domain of nicotinic acetylcholine receptor
Q60034625	NR3E receptors in cnidarians: A new family of steroid receptor relatives extends the possible mechanisms for ligand binding
Q30925874	Natural Disulfide Bond-disrupted Mutants of AVR4 of the Tomato Pathogen Cladosporium fulvum Are Sensitive to Proteolysis, Circumvent Cf-4-mediated Resistance, but Retain Their Chitin Binding Ability
Q91526716	Natural Product Inspired Novel Indole based Chiral Scaffold Kills Human Malaria Parasites via Ionic Imbalance Mediated Cell Death
Q34058067	Near-native protein loop sampling using nonparametric density estimation accommodating sparcity
Q49804506	New Bacterial Phytase through Metagenomic Prospection.
Q89497041	New Deep Learning Methods for Protein Loop Modeling
Q35686667	New aryl hydrocarbon receptor homology model targeted to improve docking reliability
Q30362525	Nonbonded terms extrapolated from nonlocal knowledge-based energy functions improve error detection in near-native protein structure models.
Q47312800	Nonsteroidal estrogen receptor isoform-selective biphenyls
Q40048925	Novel Organelles with Elements of Bacterial and Eukaryotic Secretion Systems Weaponize Parasites of Drosophila
Q35570052	Novel inhibitors of Mycobacterium tuberculosis dTDP-6-deoxy-L-lyxo-4-hexulose reductase (RmlD) identified by virtual screening
Q36776553	Novel insights into CB1 cannabinoid receptor signaling: a key interaction identified between the extracellular-3 loop and transmembrane helix 2
Q51808069	Novel mutants of the human beta1-adrenergic receptor reveal amino acids relevant for receptor activation.
Q57077664	Nucleotide recognition by the initiation factor aIF5B: Free energy simulations of a neoclassical GTPase
Q36702740	Nucleotide-dependent control of internal strains in ring-shaped AAA+ motors
Q36851694	OPUS-Rota: a fast and accurate method for side-chain modeling
Q30157331	One membrane protein, two structures and six environments: a comparative molecular dynamics simulation study of the bacterial outer membrane protein PagP.
Q62599579	Open-Boundary Molecular Mechanics/Coarse-Grained Framework for Simulations of Low-Resolution G-Protein-Coupled Receptor-Ligand Complexes
Q35933755	Optimization of the GB/SA solvation model for predicting the structure of surface loops in proteins
Q42862591	Optimized atomic statistical potentials: assessment of protein interfaces and loops
Q28535193	Organism-adapted specificity of the allosteric regulation of pyruvate kinase in lactic acid bacteria
Q28485154	Oroxylin A inhibits hemolysis via hindering the self-assembly of α-hemolysin heptameric transmembrane pore
Q47133897	Outer membrane protein folding from an energy landscape perspective
Q30157953	Outer membrane proteins: comparing X-ray and NMR structures by MD simulations in lipid bilayers.
Q34432049	PDZ binding to the BAR domain of PICK1 is elucidated by coarse-grained molecular dynamics
Q41872855	PIK3CA somatic mutations in breast cancer: Mechanistic insights from Langevin dynamics simulations
Q34302452	Parallel molecular evolution in an herbivore community
Q42620532	Partial characterization of an atypical family I inorganic pyrophosphatase from cattle tick Rhipicephalus (Boophilus) microplus.
Q35223328	Phospholipid binding residues of eukaryotic membrane-remodelling F-BAR domain proteins are conserved in Helicobacter pylori CagA
Q35625043	Phosphorylation of PPARγ Affects the Collective Motions of the PPARγ-RXRα-DNA Complex
Q39033584	Phosphorylation regulates the assembly of chloroplast import machinery.
Q28242771	Physicochemical characterization and functional site analysis of lactoferrin gene of Vechur cow
Q48715103	Platelets contribute to amyloid-β aggregation in cerebral vessels through integrin αIIbβ3-induced outside-in signaling and clusterin release.
Q100958562	Polymerization and editing modes of a high-fidelity DNA polymerase are linked by a well-defined path
Q41906900	Population shift of binding pocket size and dynamic correlation analysis shed new light on the anticooperative mechanism of PII protein
Q51514706	Predicting antibody complementarity determining region structures without classification.
Q54124846	Predicting the Conformational Variability of Abl Tyrosine Kinase using Molecular Dynamics Simulations and Markov State Models.
Q92594361	Prediction of Conformation Specific Thermostabilizing Mutations for Class A G Protein-Coupled Receptors
Q36870684	Prediction of Protein Loop Conformations using the AGBNP Implicit Solvent Model and Torsion Angle Sampling
Q47625069	Prediction of binding poses to FXR using multi-targeted docking combined with molecular dynamics and enhanced sampling.
Q37002751	Prediction of protein loop structures using a local move Monte Carlo approach and a grid-based force field
Q41944897	Prediction of the odorant binding site of olfactory receptor proteins by human-mouse comparisons
Q41934691	Prediction of the three-dimensional structure of serine/threonine protein kinase pto of Solanum lycopersicum by homology modelling
Q30571286	Probing large conformational rearrangements in wild-type and mutant spectrin using structural mass spectrometry
Q34280087	Probing molecular mechanisms of the Hsp90 chaperone: biophysical modeling identifies key regulators of functional dynamics
Q46427567	Probing the beta2 adrenoceptor binding site with catechol reveals differences in binding and activation by agonists and partial agonists
Q35013538	Probing the carboxyester side chain in controlled deactivation (-)-δ(8)-tetrahydrocannabinols
Q44020919	Probing the specificity of a trypanosomal aromatic alpha-hydroxy acid dehydrogenase by site-directed mutagenesis
Q41832861	Probing the steric space at the floor of the D1 dopamine receptor orthosteric binding domain: 7α-, 7β-, 8α-, and 8β-methyl substituted dihydrexidine analogues
Q38915827	Progress in super long loop prediction.
Q57075261	Protein Homology Modelling
Q40518742	Protein fragment reconstruction using various modeling techniques
Q34097299	Protein loop closure using orientational restraints from NMR data
Q34292837	Protein loop modeling by using fragment assembly and analytical loop closure
Q30368895	Protein loop modeling using a new hybrid energy function and its application to modeling in inaccurate structural environments.
Q51568651	Protein loop selection using orientation-dependent force fields derived by parameter optimization.
Q30367773	Protein structure fitting and refinement guided by cryo-EM density
Q30374281	Protein structure homology modeling using SWISS-MODEL workspace.
Q30350916	Protein structure modeling in the proteomics era.
Q30366789	Protein structure prediction provides comparable performance to crystallographic structures in docking-based virtual screening.
Q30327771	Protein structure prediction.
Q30409913	Protein structure validation by generalized linear model root-mean-square deviation prediction
Q63610134	Protonation of the Biliverdin IXα Chromophore in the Red and Far-Red Photoactive States of a Bacteriophytochrome
Q52315092	Quantitative interaction analysis permits molecular insights into functional NOX4 NADPH oxidase heterodimer assembly.
Q30552721	RNA polymerase II flexibility during translocation from normal mode analysis
Q34206064	RNA polymerase II with open and closed trigger loops: active site dynamics and nucleic acid translocation
Q24813293	RPBS: a web resource for structural bioinformatics
Q35187652	Rationalizing 5000-fold differences in receptor-binding rate constants of four cytokines
Q41906114	Rationalizing the evolution of EAL domain-based cyclic di-GMP-specific phosphodiesterases
Q38035620	Re-engineered stromal cell-derived factor-1α and the future of translatable angiogenic polypeptide design
Q36329533	Receptor-guided 3D-QSAR studies, molecular dynamics simulation and free energy calculations of Btk kinase inhibitors
Q38952944	Recovery and purification of oligosaccharides from copra meal by recombinant endo-β-mannanase and deciphering molecular mechanism involved and its role as potent therapeutic agent
Q30385763	Refinement of atomic models in high resolution EM reconstructions using Flex-EM and local assessment.
Q37733388	Regulation of the epithelial Na+ channel and airway surface liquid volume by serine proteases
Q33455669	Regulatory elements within the prodomain of Falcipain-2, a cysteine protease of the malaria parasite Plasmodium falciparum
Q34786682	Remote thioredoxin recognition using evolutionary conservation and structural dynamics
Q34562722	Residue-specific annotation of disorder-to-order transition and cathepsin inhibition of a propeptide-like crammer from D. melanogaster
Q36685036	Residues accessible in the binding-site crevice of transmembrane helix 6 of the CB2 cannabinoid receptor
Q48165482	Revealing the Roles of Subdomains in the Catalytic Behavior of Lipases/Acyltransferases Homologous to CpLIP2 through Rational Design of Chimeric Enzymes
Q44062393	Reversible covalent inhibition of eEF-2K by carbonitriles.
Q35671871	Rice stripe1-2 and stripe1-3 Mutants Encoding the Small Subunit of Ribonucleotide Reductase Are Temperature Sensitive and Are Required for Chlorophyll Biosynthesis
Q54516010	Role of Cys73 in the thermostability of farnesyl diphosphate synthase from Geobacillus stearothermophilus.
Q35758611	Role of group-conserved residues in the helical core of beta2-adrenergic receptor
Q87404860	Role of pH in structural changes for Pin1 protein: an insight from molecular dynamics study
Q44938119	Rotor/Stator interactions of the epsilon subunit in Escherichia coli ATP synthase and implications for enzyme regulation.
Q41957147	SELECTpro: effective protein model selection using a structure-based energy function resistant to BLUNDERs
Q30976450	SKPDB: a structural database of shikimate pathway enzymes.
Q41724483	SL2: an interactive webtool for modeling of missing segments in proteins
Q27301335	SPATA5 mutations cause a distinct autosomal recessive phenotype of intellectual disability, hypotonia and hearing loss
Q34097102	SWIFT MODELLER v2.0: a platform-independent GUI for homology modeling.
Q33801115	SWIFT MODELLER: a Java based GUI for molecular modeling.
Q27937861	Saccharomyces cerevisiae Npc2p is a functionally conserved homologue of the human Niemann-Pick disease type C 2 protein, hNPC2.
Q36445595	Salmon-derived thrombin inhibits development of chronic pain through an endothelial barrier protective mechanism dependent on APC.
Q35536457	Sampling multiple scoring functions can improve protein loop structure prediction accuracy
Q30355331	Saturating representation of loop conformational fragments in structure databanks
Q58615492	Selectivity and Promiscuity in TET-mediated oxidation of 5-methylcytosine in DNA and RNA
Q42943551	Self-assembly of a simple membrane protein: coarse-grained molecular dynamics simulations of the influenza M2 channel.
Q89892709	Semi-synthetic cinnamodial analogues: Structural insights into the insecticidal and antifeedant activities of drimane sesquiterpenes against the mosquito Aedes aegypti
Q33510934	Sequence and structure signatures of cancer mutation hotspots in protein kinases
Q53549086	Sequence requirements for splicing by the Cne PRP8 intein.
Q42921968	Sequence-structure relationships in RNA loops: establishing the basis for loop homology modeling
Q91637313	Shank3 Mice Carrying the Human Q321R Mutation Display Enhanced Self-Grooming, Abnormal Electroencephalogram Patterns, and Suppressed Neuronal Excitability and Seizure Susceptibility
Q30373871	Sigma-RF: prediction of the variability of spatial restraints in template-based modeling by random forest.
Q90737791	Simple Selection Procedure to Distinguish between Static and Flexible Loops
Q28481334	Simulating molecular mechanisms of the MDM2-mediated regulatory interactions: a conformational selection model of the MDM2 lid dynamics
Q36033903	Simulations of the p97 complex suggest novel conformational states of hydrolysis intermediates
Q54960290	Site-Mutation of Hydrophobic Core Residues Synchronically Poise Super Interleukin 2 for Signaling: Identifying Distant Structural Effects through Affordable Computations.
Q34697680	Site-directed amino acid substitutions in the hydroxylase alpha subunit of butane monooxygenase from Pseudomonas butanovora: Implications for substrates knocking at the gate
Q34012132	Small molecule chemokine mimetics suggest a molecular basis for the observation that CXCL10 and CXCL11 are allosteric ligands of CXCR3
Q59137841	Small-angle neutron scattering studies on the AMPA receptor GluA2 in the resting, AMPA-bound and GYKI-53655-bound states
Q35470475	Solution X-ray scattering combined with computational modeling reveals multiple conformations of covalently bound ubiquitin on PCNA
Q35080400	Solution structure of the complex between poxvirus-encoded CC chemokine inhibitor vCCI and human MIP-1beta.
Q51616768	Species extrapolation for the 21st century.
Q61928097	Specific cardiolipin-SecY interactions are required for proton-motive force stimulation of protein secretion
Q36893404	Specific ligand binding domain residues confer low dioxin responsiveness to AHR1β of Xenopus laevis
Q35182886	Spectrin-like repeats 11-15 of human dystrophin show adaptations to a lipidic environment
Q38814529	Sphinx: merging knowledge-based and ab initio approaches to improve protein loop prediction
Q24644665	Stabilized phosphatidylinositol-5-phosphate analogues as ligands for the nuclear protein ING2: chemistry, biology, and molecular modeling
Q29615145	Statistical potential for assessment and prediction of protein structures
Q35635713	Statistical potential for modeling and ranking of protein-ligand interactions
Q30329417	Statistical potentials for fold assessment.
Q51421152	Stiffness of the C-terminal disordered linker affects the geometry of the active site in endoglucanase Cel8A.
Q27683319	Structural Analysis of Replication Protein A Recruitment of the DNA Damage Response Protein SMARCAL1
Q57014374	Structural Domains and Main-Chain Flexibility in Prion Proteins†
Q47269444	Structural analysis of the envelope gp120 V3 loop for some HIV-1 variants circulating in the countries of Eastern Europe
Q27676099	Structural and Functional Analysis of the DEAF-1 and BS69 MYND Domains
Q27649433	Structural and Functional Relationships in the Virulence-associated Cathepsin L Proteases of the Parasitic Liver Fluke, Fasciola hepatica
Q58549084	Structural and dynamic basis of substrate permissiveness in hydroxycinnamoyltransferase (HCT)
Q33815254	Structural and functional characterization of the aryl hydrocarbon receptor ligand binding domain by homology modeling and mutational analysis
Q64963144	Structural and functional consequences of the STAT5BN642H driver mutation.
Q57752379	Structural bases of GM1 gangliosidosis and Morquio B disease
Q83230233	Structural basis for AcrVA4 inhibition of specific CRISPR-Cas12a
Q27690046	Structural basis for assembly and function of a heterodimeric plant immune receptor
Q41329955	Structural basis for interdomain communication in SHIP2 providing high phosphatase activity
Q36458400	Structural basis for the enantiospecificities of R- and S-specific phenoxypropionate/alpha-ketoglutarate dioxygenases
Q38734550	Structural basis of activation of bitter taste receptor T2R1 and comparison with Class A G-protein-coupled receptors (GPCRs)
Q44538982	Structural basis of the lisinopril-binding specificity in N- and C-domains of human somatic ACE.
Q33818899	Structural basis to stabilize the domain motion of BARD1-ARD BRCT by CstF50.
Q41771777	Structural determinants allowing transferase activity in SENSITIVE TO FREEZING 2, classified as a family I glycosyl hydrolase
Q35838161	Structural determinants of the alpha2 adrenoceptor subtype selectivity
Q34918704	Structural effects of quinacrine binding in the open channel of the acetylcholine receptor.
Q38810210	Structural features of cytochrome P450 1A associated with the absence of EROD activity in liver of the loricariid catfish Pterygoplichthys sp.
Q35204026	Structural genomics: computational methods for structure analysis
Q36796209	Structural insights and functional implications of inter-individual variability in β2-adrenergic receptor
Q28481687	Structural insights from binding poses of CCR2 and CCR5 with clinically important antagonists: a combined in silico study
Q24337478	Structural insights into the catalytic active site and activity of human Nit2/ω-amidase: kinetic assay and molecular dynamics simulation
Q42716640	Structural mechanism associated with domain opening in gain-of-function mutations in SHP2 phosphatase.
Q27655494	Structural mechanism of SDS-induced enzyme activity of scorpion hemocyanin revealed by electron cryomicroscopy
Q34326572	Structural modeling and DNA binding autoinhibition analysis of Ergp55, a critical transcription factor in prostate cancer.
Q38845142	Structural modeling of the AhR:ARNT complex in the bHLH-PASA-PASB region elucidates the key determinants of dimerization.
Q34639481	Structural models of TREK channels and their gating mechanism
Q34508341	Structural proteomics: developments in structure-to-function predictions
Q42691972	Structural states of the flexible catalytic loop of M. tuberculosis tyrosyl-tRNA synthetase in different enzyme-substrate complexes
Q56967108	Structure and Mechanisms of NT5C2 Mutations Driving Thiopurine Resistance in Relapsed Lymphoblastic Leukemia
Q104073530	Structure and dynamics of an α-fucosidase reveal a mechanism for highly efficient IgG transfucosylation
Q40009167	Structure modeling and functional analysis of recombinant dextransucrase from Weissella confusa Cab3 expressed in Lactococcus lactis
Q34179300	Structure modeling of the chemokine receptor CCR5: implications for ligand binding and selectivity
Q30437093	Structure of human Rad51 protein filament from molecular modeling and site-specific linear dichroism spectroscopy
Q27703282	Structure of human heat-shock transcription factor 1 in complex with DNA
Q27642825	Structure of nucleotide-binding domain 1 of the cystic fibrosis transmembrane conductance regulator
Q30390812	Structure of pleiotrophin- and hepatocyte growth factor-binding sulfated hexasaccharide determined by biochemical and computational approaches
Q89723022	Structure of the agonist 12-HHT in its BLT2 receptor-bound state
Q36035334	Structure prediction of loops with fixed and flexible stems
Q37165240	Structure-Based, Rational Design of T Cell Receptors
Q47407059	Structure-based assessment of missense mutations in human BRCA1: implications for breast and ovarian cancer predisposition
Q80162928	Structure-based calculation of binding affinities of alpha 2A-adrenoceptor agonists
Q36092090	Structure-based identification and characterisation of structurally novel human P2X7 receptor antagonists
Q30368961	Structure-based network analysis of activation mechanisms in the ErbB family of receptor tyrosine kinases: the regulatory spine residues are global mediators of structural stability and allosteric interactions.
Q42817627	Structure-cytotoxicity relationships in bovine seminal ribonuclease: new insights from heat and chemical denaturation studies on variants
Q27300779	Structure-function features of a Mycoplasma glycolipid synthase derived from structural data integration, molecular simulations, and mutational analysis
Q47389316	Structures of Dynamic Protein Complexes: Hybrid Techniques to Study MAP Kinase Complexes and the ESCRT System
Q91817101	Studies of structural determinants of substrate binding in the Creatine Transporter (CreaT, SLC6A8) using molecular models
Q46778878	Study on the enantioselectivity inhibition mechanism of acetyl-coenzyme A carboxylase toward haloxyfop by homology modeling and MM-PBSA analysis
Q30482731	Subnanometer-resolution electron cryomicroscopy-based domain models for the cytoplasmic region of skeletal muscle RyR channel
Q51769186	Substituted pyrazolo[3,4-b]pyridines as human A1 adenosine antagonists: developments in understanding the receptor stereoselectivity.
Q33323622	Substituted pyrazolo[3,4-b]pyridines as potent A1 adenosine antagonists: synthesis, biological evaluation, and development of an A1 bovine receptor model
Q35002989	Successful prediction of the intra- and extracellular loops of four G-protein-coupled receptors
Q30382391	Symmetry-restrained molecular dynamics simulations improve homology models of potassium channels
Q30370706	Systematic analysis of the effect of multiple templates on the accuracy of comparative models of protein structure.
Q30361719	TAP score: torsion angle propensity normalization applied to local protein structure evaluation.
Q35128951	TASSER-Lite: an automated tool for protein comparative modeling
Q34066957	TCRep 3D: an automated in silico approach to study the structural properties of TCR repertoires
Q36096947	Target molecular simulations of RecA family protein filaments
Q30382761	Template-based protein modeling: recent methodological advances.
Q24561937	Template-based protein structure modeling
Q34187374	Tertiary structure predictions on a comprehensive benchmark of medium to large size proteins
Q30855420	The CaMKII holoenzyme structure in activation-competent conformations
Q34489039	The Dynamic Process of Drug-GPCR Binding at Either Orthosteric or Allosteric Sites Evaluated by Metadynamics
Q45393755	The F130L mutation in streptavidin reduces its binding affinity to biotin through electronic polarization effect.
Q28484433	The Ionic and hydrophobic interactions are required for the auto activation of cysteine proteases of Plasmodium falciparum
Q36090299	The KDEL receptor couples to Gαq/11 to activate Src kinases and regulate transport through the Golgi
Q28756561	The N-clasp of human DNA polymerase kappa promotes blockage or error-free bypass of adenine- or guanine-benzo[a]pyrenyl lesions
Q27675216	The NMR structure of stomagen reveals the basis of stomatal density regulation by plant peptide hormones
Q58995298	The P25 Ookinete Surface Proteins: Homology Modeling and Phylogenetic Relationships
Q28592152	The PINIT domain of PIAS3: structure-function analysis of its interaction with STAT3
Q51306761	The Parasol Protocol for computational mutagenesis.
Q42136906	The RNF168 paralog RNF169 defines a new class of ubiquitylated histone reader involved in the response to DNA damage.
Q27681019	The Solution Structure of the Regulatory Domain of Tyrosine Hydroxylase
Q27666503	The Structure of Lombricine Kinase: IMPLICATIONS FOR PHOSPHAGEN KINASE CONFORMATIONAL CHANGES
Q24300764	The TCL1 oncoprotein binds the RNase PH domains of the PNPase exoribonuclease without affecting its RNA degrading activity
Q30406909	The VSGB 2.0 model: a next generation energy model for high resolution protein structure modeling
Q37263172	The common hereditary elliptocytosis-associated α-spectrin L260P mutation perturbs erythrocyte membranes by stabilizing spectrin in the closed dimer conformation.
Q41816098	The complex and specific pMHC interactions with diverse HIV-1 TCR clonotypes reveal a structural basis for alterations in CTL function
Q47566645	The dynamic mechanism of RASSF5 and MST kinase activation by Ras.
Q30389150	The effect of chirality and steric hindrance on intrinsic backbone conformational propensities: tools for protein design
Q40283388	The effect of end constraints on protein loop kinematics
Q31038185	The energy landscape analysis of cancer mutations in protein kinases
Q34102711	The flexible C-terminal arm of the Lassa arenavirus Z-protein mediates interactions with multiple binding partners
Q47766846	The fused SnoaL_2 domain in the Mycobacterium tuberculosis sigma factor σJ modulates promoter recognition
Q37198485	The importance of slow motions for protein functional loops
Q46943391	The lactate dehydrogenases encoded by the ldh and ldhB genes in Lactococcus lactis exhibit distinct regulation and catalytic properties - comparative modeling to probe the molecular basis
Q38652200	The length but not the sequence of peptide linker modules exerts the primary influence on the conformations of protein domains in cellulosome multi-enzyme complexes.
Q53562093	The major secreted cathepsin L1 protease of the liver fluke, Fasciola hepatica: a Leu-12 to Pro-12 replacement in the nonconserved C-terminal region of the prosegment prevents complete enzyme autoactivation and allows definition of the molecular eve
Q52652201	The molecular basis of the differential subcellular localization of FYVE domains.
Q90323496	The novel BET-CBP/p300 dual inhibitor NEO2734 is active in SPOP mutant and wild-type prostate cancer
Q47160580	The orientation and stability of the GPCR-Arrestin complex in a lipid bilayer.
Q36955733	The origin of the cooperativity in the streptavidin-biotin system: A computational investigation through molecular dynamics simulations
Q42431612	The pH-dependent Client Release from the Collagen-specific Chaperone HSP47 Is Triggered by a Tandem Histidine Pair
Q61001486	The phenylketonuria-associated substitution R68S converts phenylalanine hydroxylase to a constitutively active enzyme but reduces its stability.
Q22248093	The protein structure prediction problem could be solved using the current PDB library
Q33974538	The quaternary structure of the Saccharomyces cerevisiae succinate dehydrogenase. Homology modeling, cofactor docking, and molecular dynamics simulation studies
Q35733326	The second extracellular loop of the dopamine D2 receptor lines the binding-site crevice
Q34170768	The second sodium site in the dopamine transporter controls cation permeation and is regulated by chloride
Q39904811	The structure of p85ni in class IA phosphoinositide 3-kinase exhibits interdomain disorder
Q46396844	The susceptible HLA class II alleles and their presenting epitope(s) in Goodpasture's disease.
Q46272621	The zebrafish forkhead transcription factor Foxi1 specifies epibranchial placode-derived sensory neurons
Q46646720	The α7 nicotinic acetylcholine receptor: molecular modelling, electrostatics, and energetics.
Q34488477	Theoretical investigation on structural, functional and epitope of a 12 kDa excretory-secretory protein from Toxoplasma gondii.
Q37240247	Thiazolidinediones mimic glucose starvation in facilitating Sp1 degradation through the up-regulation of beta-transducin repeat-containing protein
Q42174754	Three Dimensional Structure Prediction of Fatty Acid Binding Site on Human Transmembrane Receptor CD36
Q74818940	Three-dimensional representations of G protein-coupled receptor structures and mechanisms
Q30333054	Tools for comparative protein structure modeling and analysis
Q81305424	Toward Mycobacterium tuberculosis DXR inhibitor design: homology modeling and molecular dynamics simulations
Q42585482	Toward better refinement of comparative models: predicting loops in inexact environments
Q30369585	Toward the virtual screening of Cdc25A phosphatase inhibitors with the homology modeled protein structure.
Q91924492	Towards A Molecular Understanding of The Cannabinoid Related Orphan Receptor GPR18: A Focus on Its Constitutive Activity
Q34611560	Towards improved quality of GPCR models by usage of multiple templates and profile-profile comparison
Q30408234	Transmembrane domains of attraction on the TSH receptor
Q37282203	Transmembrane helical domain of the cannabinoid CB1 receptor
Q58720139	Tubulin's response to external electric fields by molecular dynamics simulations
Q33279689	Tyr66 acts as a conformational switch in the closed-to-open transition of the SHP-2 N-SH2-domain phosphotyrosine-peptide binding cleft.
Q30523971	UCSF Chimera, MODELLER, and IMP: an integrated modeling system
Q35102121	Unbiased, scalable sampling of protein loop conformations from probabilistic priors
Q30494445	Unidirectional Brownian motion observed in an in silico single molecule experiment of an actomyosin motor
Q39923654	Unlocking the Bacterial SecY Translocon
Q27351194	Uracil DNA N-glycosylase promotes assembly of human centromere protein A
Q24803200	Use of a structural alphabet for analysis of short loops connecting repetitive structures
Q30432695	Validating a Coarse-Grained Potential Energy Function through Protein Loop Modelling
Q30410854	Virtual ligand screening against comparative protein structure models
Q40563969	pH-sensitive residues in the p19 RNA silencing suppressor protein from carnation Italian ringspot virus affect siRNA binding stability

P356	DOI	10.1110/PS.9.9.1753
P3181	OpenCitations bibliographic resource ID	477218
P932	PMC publication ID	2144714
P698	PubMed publication ID	11045621
P5875	ResearchGate publication ID	12278118

P2093	author name string	Sali A
		Fiser A
		Do RK
P2860	cites work	Large-scale protein structure modeling of the Saccharomyces cerevisiae genome	Q24654088
		Protein engineering with monomeric triosephosphate isomerase (monoTIM): the modelling and structure verification of a seven-residue loop	Q27735188
		Crystal structure of the delta' subunit of the clamp-loader complex of E. coli DNA polymerase III	Q27747193
		Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features	Q27860675
		Comparative protein structure modeling of genes and genomes	Q27860712
		Comparative protein modelling by satisfaction of spatial restraints	Q27860866
		Stereochemistry of polypeptide chain configurations	Q28190300
		Conformation of beta-hairpins in protein structures. A systematic classification with applications to modelling by homology, electron density fitting and protein engineering	Q28243575
		Recognition of errors in three-dimensional structures of proteins	Q28249658
		Conformations of immunoglobulin hypervariable regions	Q28273335
		Fold and function predictions for Mycoplasma genitalium proteins	Q28280035
		Assessment of protein models with three-dimensional profiles	Q28283805
		Ligand specificity of brain lipid-binding protein	Q28289448
		Accurate modeling of protein conformation by automatic segment matching	Q28290861
		Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes	Q28305615
		Database of homology-derived protein structures and the structural meaning of sequence alignment	Q29614393
		Structural basis of substrate specificity in the serine proteases	Q29619675
		GenTHREADER: an efficient and reliable protein fold recognition method for genomic sequences	Q29620735
		Modelling the polypeptide backbone with 'spare parts' from known protein structures	Q30196043
		Are predicted structures good enough to preserve functional sites?	Q30322788
		Critical assessment of methods of protein structure prediction (CASP): round III.	Q30323113
		ModBase: a database of comparative protein structure models.	Q30326459
		Taxonomy and conformational analysis of loops in proteins.	Q30350131
		Structure of antibody hypervariable loops reproduced by a conformational search algorithm	Q30404853
		The consistency principle in protein structure and pathways of folding	Q30413244
		Prediction of protein three-dimensional structures in insertion and deletion regions: a procedure for searching data bases of representative protein fragments using geometric scoring criteria.	Q30416560
		The main-chain dynamics of the dynamin pleckstrin homology (PH) domain in solution: analysis of 15N relaxation with monomer/dimer equilibration 1 1 Edited by P.E.Wright	Q58175598
		Analysis of insertions/deletions in protein structures	Q68092010
		Anti-insulin antibody structure and conformation. II. Molecular dynamics with explicit solvent	Q68181844
		Conformational sampling using high-temperature molecular dynamics	Q68545089
		Predicting antibody hypervariable loop conformation. I. Ensembles of random conformations for ringlike structures	Q68557407
		Predicting antibody hypervariable loop conformations. II: Minimization and molecular dynamics studies of MCPC603 from many randomly generated loop conformations	Q68704284
		Canonical structures for the hypervariable regions of immunoglobulins	Q69450418
		Turn prediction in proteins using a pattern-matching approach	Q69610320
		Prediction of the folding of short polypeptide segments by uniform conformational sampling	Q69715633
		The predicted structure of immunoglobulin D1.3 and its comparison with the crystal structure	Q70300738
		A critical assessment of comparative molecular modeling of tertiary structures of proteins	Q71267484
		Protein-protein interaction at crystal contacts	Q71374340
		Comparison of an antibody model with an X-ray structure: the variable fragment of BR96	Q71565956
		Analysis of two-residue turns in proteins	Q72418886
		Molecular dynamics of native protein. II. Analysis and nature of motion	Q72709889
		Improvement of turn structure prediction by molecular dynamics: a case study of alpha 1-purothionin	Q72777492
		Homology modeling with internal coordinate mechanics: deformation zone mapping and improvements of models via conformational search	Q74252568
		Chameleon sequences in the PDB	Q77188533
		Prediction of loop geometries using a generalized born model of solvation effects	Q77386247
		100,000 protein structures for the biologist	Q77659489
		Modeling the anti-CEA antibody combining site by homology and conformational search	Q46604797
		Predicting the conformational class of short and medium size loops connecting regular secondary structures: application to comparative modelling	Q47311954
		Three-dimensional structure analysis of PROSITE patterns	Q47623945
		Homology-based fold predictions for Mycoplasma genitalium proteins	Q47625370
		Prediction of protein-protein interaction sites using patch analysis	Q47627162
		Assessment of comparative modeling in CASP2.	Q47628125
		Structural families in loops of homologous proteins: automatic classification, modelling and application to antibodies	Q47628564
		Automatic classification and analysis of alpha alpha-turn motifs in proteins	Q47630201
		Common features of the conformations of antigen-binding loops in immunoglobulins and application to modeling loop conformations	Q47637017
		Structural determinants of the conformations of medium-sized loops in proteins	Q47643263
		Supersites within superfolds. Binding site similarity in the absence of homology	Q47749122
		ABGEN: a knowledge-based automated approach for antibody structure modeling	Q47961159
		A global taxonomy of loops in globular proteins.	Q48785741
		A novel exhaustive search algorithm for predicting the conformation of polypeptide segments in proteins.	Q52078677
		Free energy landscapes of peptides by enhanced conformational sampling.	Q52082381
		New efficient statistical sequence-dependent structure prediction of short to medium-sized protein loops based on an exhaustive loop classification.	Q52211558
		Functional analysis of the Escherichia coli genome using the sequence-to-structure-to-function paradigm: identification of proteins exhibiting the glutaredoxin/thioredoxin disulfide oxidoreductase activity.	Q52235911
		PDB-based protein loop prediction: parameters for selection and methods for optimization.	Q52267152
		Prediction of hypervariable CDR-H3 loop structures in antibodies.	Q52346621
		Predicting immunoglobulin-like hypervariable loops.	Q52364201
		The loop problem in proteins: a Monte Carlo simulated annealing approach.	Q52393085
		Exhaustive conformational search and simulated annealing for models of lattice peptides.	Q52399960
		Empirical and structural models for insertions and deletions in the divergent evolution of proteins.	Q52400709
		Development of an extended simulated annealing method: Application to the modeling of complementary determining regions of immunoglobulins	Q52430167
		Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins.	Q52451138
		An automated classification of the structure of protein loops.	Q53972089
		Multiple copy sampling: rigid versus flexible protein.	Q54026445
		Evaluation of the conformational free energies of loops in proteins.	Q54641591
		Similarities between protein 3-D structures	Q57013707
		Novel knowledge-based mean force potential at atomic level	Q57977731
		Simultaneous modeling of multiple loops in proteins	Q30416879
		Comparison of systematic search and database methods for constructing segments of protein structure	Q30418808
		Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins	Q30421728
		Origins of structural diversity within sequentially identical hexapeptides	Q30421773
		Fragment ranking in modelling of protein structure. Conformationally constrained environmental amino acid substitution tables.	Q30422505
		Advances in comparative protein-structure modelling	Q30426879
		Evaluation of comparative protein structure modeling by MODELLER-3.	Q30429627
		A graph-theoretic algorithm for comparative modeling of protein structure	Q30430781
		Recognition of spatial motifs in protein structures	Q30432556
		CASP3 comparative modeling evaluation	Q30794909
		Enhanced conformational sampling in Monte Carlo simulations of proteins: application to a constrained peptide	Q33877281
		Knowledge-based prediction of protein structures and the design of novel molecules	Q34183412
		Modeling of globular proteins. A distance-based data search procedure for the construction of insertion/deletion regions and Pro----non-Pro mutations	Q34292073
		Modeling antibody hypervariable loops: a combined algorithm.	Q34322701
		Structure-based inhibitor design by using protein models for the development of antiparasitic agents	Q36252297
		Comparison of conformational characteristics in structurally similar protein pairs	Q36277752
		De novo prediction of polypeptide conformations using dihedral probability grid Monte Carlo methodology	Q36279222
		Conformational analysis and clustering of short and medium size loops connecting regular secondary structures: a database for modeling and prediction	Q36279619
		Model for haptoglobin heavy chain based upon structural homology	Q36393459
		A self consistent mean field approach to simultaneous gap closure and side-chain positioning in homology modelling	Q36678466
		Structure-based design and combinatorial chemistry yield low nanomolar inhibitors of cathepsin D.	Q36867191
		Functional significance of loops in the receptor binding domain of Bacillus thuringiensis CryIIIA delta-endotoxin	Q38361914
		A possible three-dimensional structure of bovine α-lactalbumin based on that of hen's egg-white lysozyme	Q38363100
		Mapping protein dynamics by X-ray diffraction	Q39823346
		A structural explanation for the twilight zone of protein sequence homology	Q40923201
		Accuracy and reliability of the scaling-relaxation method for loop closure: an evaluation based on extensive and multiple copy conformational samplings	Q40950814
		Engineering metal-binding sites in proteins	Q41573414
		Flexible ligand docking: a multistep strategy approach	Q41673303
		Multiple copy sampling in protein loop modeling: computational efficiency and sensitivity to dihedral angle perturbations	Q41824327
		Modeling of protein loops by simulated annealing	Q42065147
		Prediction of the location and type of beta-turns in proteins using neural networks.	Q42133058
		Using known substructures in protein model building and crystallography	Q42253437
		Structural motif of phosphate-binding site common to various protein superfamilies: all-against-all structural comparison of protein-mononucleotide complexes	Q42594583
		Protein-DNA interactions: A structural analysis	Q42600123
		Computing the structure of bound peptides. Application to antigen recognition by class I major histocompatibility complex receptors	Q42610228
		Determining protein loop conformation using scaling-relaxation techniques	Q42843145
		Modeling protein loops using a phi i + 1, psi i dimer database	Q42844816
		Does conformational free energy distinguish loop conformations in proteins?	Q42929125
		Search for the stable state of a short chain in a molecular field	Q43458590
		Determining minimum energy conformations of polypeptides by dynamic programming	Q44959156
		An algorithm for determining the conformation of polypeptide segments in proteins by systematic search	Q45559122
P433	issue	9
P407	language of work or name	English	Q1860
P304	page(s)	1753-73
P577	publication date	2000-09-01
P1433	published in	Protein Science	Q7251445
P1476	title	Modeling of loops in protein structures
P2283	uses	MODELLER	Q3859815
P478	volume	9

Modeling of loops in protein structures

scientific article (publication date: September 2000)

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