Exploring protein native states and large-scale conformational changes with a modified generalized born model (scientific article (publication date: May 2004))

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Q34801749	Equilibrium and folding simulations of NS4B H2 in pure water and water/2,2,2-trifluoroethanol mixed solvent: examination of solvation models
Q88055732	Escape of a Small Molecule from Inside T4 Lysozyme by Multiple Pathways
Q43888998	Evaluation and binding-mode prediction of thiopyrone-based inhibitors of anthrax lethal factor
Q38848165	Evaluation of DNA Force Fields in Implicit Solvation
Q37518530	Evaluation of DOCK 6 as a pose generation and database enrichment tool
Q46829757	Evaluation of the 'side door' in carboxylesterase-mediated catalysis and inhibition
Q42212022	Evidence for an electrostatic mechanism of force generation by the bacteriophage T4 DNA packaging motor.
Q47595845	Evolution of conformational dynamics determines the conversion of a promiscuous generalist into a specialist enzyme.
Q51654036	Examination of the quality of various force fields and solvation models for the equilibrium simulations of GA88 and GB88.
Q38724928	Experimental and computational insights on the recognition mechanism between the estrogen receptor α with bisphenol compounds
Q57301293	Explicit ions/implicit water generalized Born model for nucleic acids
Q47934946	Exploring Binding Mechanisms in Nuclear Hormone Receptors by Monte Carlo and X-ray-derived Motions
Q93190439	Exploring Novel N-Myristoyltransferase Inhibitors: A Molecular Dynamics Simulation Approach
Q92688474	Exploring benzoxaborole derivatives as carbonic anhydrase inhibitors: a structural and computational analysis reveals their conformational variability as a tool to increase enzyme selectivity
Q48061878	Exploring biomolecular energy landscapes
Q40685694	Exploring resistance mechanisms of HCV NS3/4A protease mutations to MK5172: insight from molecular dynamics simulations and free energy calculations
Q39806167	Exploring the Energy Landscapes of Cyclic Tetrapeptides with Discrete Path Sampling
Q55229082	Exploring the Interaction Mechanism Between Cyclopeptide DC3 and Androgen Receptor Using Molecular Dynamics Simulations and Free Energy Calculations.
Q39505190	Exploring the Molecular Mechanism of Cross-Resistance to HIV-1 Integrase Strand Transfer Inhibitors by Molecular Dynamics Simulation and Residue Interaction Network Analysis
Q41667510	Exploring the binding mechanisms of MIF to CXCR2 using theoretical approaches
Q57172776	Exploring the binding mechanisms of diaminopimelic acid analogs to meso-diaminopimelate dehydrogenase by molecular modeling
Q47720710	Exploring the binding sites and binding mechanism for hydrotrope encapsulated griseofulvin drug on γ-tubulin protein
Q39227396	Exploring the prominent performance of CX-4945 derivatives as protein kinase CK2 inhibitors by a combined computational study
Q33778115	Extension and validation of the GLYCAM force field parameters for modeling glycosaminoglycans
Q33784732	Extensive conformational heterogeneity within protein cores
Q53395167	Extracting ligands from receptors by reversed targeted molecular dynamics
Q51072430	Extracting representative structures from protein conformational ensembles.
Q51280448	FEW: A workflow tool for free energy calculations of ligand binding
Q51001851	Fast prediction of deleterious angiogenin mutations causing amyotrophic lateral sclerosis
Q34461976	Fatty acid-binding proteins (FABPs) are intracellular carriers for Δ9-tetrahydrocannabinol (THC) and cannabidiol (CBD).
Q53169954	Fine-tuning of microsolvation and hydrogen bond interaction regulates substrate channelling in the course of flavonoid biosynthesis
Q34307044	Folding Network of Villin Headpiece Subdomain
Q36175972	Folding and misfolding of the collagen triple helix: Markov analysis of molecular dynamics simulations
Q84629463	Folding dynamics of a small protein at room temperature via simulated coherent two-dimensional infrared spectroscopy
Q35690998	Folding free-energy landscape of villin headpiece subdomain from molecular dynamics simulations
Q30402838	Folding of Small Proteins Using Constrained Molecular Dynamics
Q37166315	Folding of Trp-cage mini protein using temperature and biasing potential replica-exchange molecular dynamics simulations
Q34649543	Folding pathways of a knotted protein with a realistic atomistic force field
Q41766036	Folding processes of the B domain of protein A to the native state observed in all-atom ab initio folding simulations
Q33598972	Folding simulations of a de novo designed protein with a betaalphabeta fold
Q30363657	Forcefield_NCAA: ab initio charge parameters to aid in the discovery and design of therapeutic proteins and peptides with unnatural amino acids and their application to complement inhibitors of the compstatin family.
Q30053209	Forcefield_PTM:Ab InitioCharge and AMBER Forcefield Parameters for Frequently Occurring Post-Translational Modifications
Q39645443	Free Energy Calculations on Snake Venom Metalloproteinase BaP1
Q50207107	Free Energy, Enthalpy and Entropy from Implicit Solvent End-Point Simulations
Q40467203	Fructose 1-phosphate is the one and only physiological effector of the Cra (FruR) regulator of Pseudomonas putida.
Q30498314	Frustration, specific sequence dependence, and nonlinearity in large-amplitude fluctuations of allosteric proteins
Q38851521	Fullerenes and their derivatives as inhibitors of tumor necrosis factor-α with highly promoted affinities
Q53605638	Functional roles of magnesium binding to extracellular signal-regulated kinase 2 explored by molecular dynamics simulations and principal component analysis
Q36072633	Further along the Road Less Traveled: AMBER ff15ipq, an Original Protein Force Field Built on a Self-Consistent Physical Model
Q51913897	GBr6NL: a generalized Born method for accurately reproducing solvation energy of the nonlinear Poisson-Boltzmann equation
Q93040742	GC ends control topology of DNA G-quadruplexes and their cation-dependent assembly
Q38830600	GPCRs through the keyhole: the role of protein flexibility in ligand binding to β-adrenoceptors.
Q90987028	GPU-Accelerated Implementation of Continuous Constant pH Molecular Dynamics in Amber: pKa Predictions with Single-pH Simulations
Q36296920	GPU/CPU Algorithm for Generalized Born/Solvent-Accessible Surface Area Implicit Solvent Calculations
Q29615867	GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit
Q50204869	Gaining insight into crizotinib resistance mechanisms caused by L2026M and G2032R mutations in ROS1 via molecular dynamics simulations and free-energy calculations
Q96771168	General population ZBTB18 missense variants influence DNA binding and transcriptional regulation
Q92277341	Generalized Born Implicit Solvent Models for Biomolecules
Q44431237	Generalized Born forces: surface integral formulation
Q48894752	Generalized Born implicit solvent models for small molecule hydration free energies
Q34287102	Generalized Born model with a simple, robust molecular volume correction
Q50999782	Geometrical constraints limiting the poly(ADP-ribose) conformation investigated by molecular dynamics simulation.
Q47781000	Girsanov reweighting for path ensembles and Markov state models
Q57153011	Global optimization of cholic acid aggregates
Q45064927	Grid-Based Surface Generalized Born Model for Calculation of Electrostatic Binding Free Energies
Q24813167	H++: a server for estimating pKas and adding missing hydrogens to macromolecules
Q92148939	HawkDock: a web server to predict and analyze the protein-protein complex based on computational docking and MM/GBSA
Q47250694	HawkRank: a new scoring function for protein-protein docking based on weighted energy terms.
Q104582419	Heparin Inhibits Cellular Invasion by SARS-CoV-2: Structural Dependence of the Interaction of the Spike S1 Receptor-Binding Domain with Heparin
Q43973455	High-Resolution HPLC–ESI–MS Characterization of the Contact Sites of the Actin–Thymosin β4 Complex by Chemical and Enzymatic Cross-Linking
Q34555853	High-resolution analysis and functional mapping of cleavage sites and substrate proteins of furin in the human proteome
Q44139271	Highlighting a π-π interaction: a protein modeling and molecular dynamics simulation study on Anopheles gambiae glutathione S-transferase 1-2.
Q51278763	Histone Acetylation Regulates Chromatin Accessibility: Role of H4K16 in Inter-nucleosome Interaction
Q35050921	Homology modeling, molecular docking, and molecular dynamics simulations elucidated α-fetoprotein binding modes
Q41671786	Host proteostasis modulates influenza evolution.
Q34075829	Hot Spots and Transient Pockets: Predicting the Determinants of Small-Molecule Binding to a Protein–Protein Interface
Q41490661	How Does the L884P Mutation Confer Resistance to Type-II Inhibitors of JAK2 Kinase: A Comprehensive Molecular Modeling Study.
Q42376486	How Water's Properties Are Encoded in Its Molecular Structure and Energies.
Q47793987	How accurate are continuum solvation models for drug-like molecules?
Q58982515	How accurate are the popular PCM/GB continuum solvation models for calculating the solvation energies of amino acid side-chain analogs?
Q35878330	How conformational dynamics of DNA polymerase select correct substrates: experiments and simulations
Q57050314	How phosphorylation influences E1 subunit pyruvate dehydrogenase: A computational study
Q37671331	How quickly can a β-hairpin fold from its transition state?
Q30492870	Human islet amyloid polypeptide monomers form ordered beta-hairpins: a possible direct amyloidogenic precursor
Q53793410	Human microtubule affinity-regulating kinase 4 is stable at extremes of pH.
Q36957378	Hydration effects on the HET-s prion and amyloid-beta fibrillous aggregates, studied with three-dimensional molecular theory of solvation
Q96765712	Hydroxamic acid derivatives as HDAC1, HDAC6 and HDAC8 inhibitors with antiproliferative activity in cancer cell lines
Q38823850	Identification of Aminoimidazole and Aminothiazole Derivatives as Src Family Kinase Inhibitors
Q34122627	Identification of a small molecule that modulates platelet glycoprotein Ib-von Willebrand factor interaction
Q84245806	Identification of folding preferences of cleavage junctions of HIV-1 precursor proteins for regulation of cleavability
Q28535326	Identification of key hinge residues important for nucleotide-dependent allostery in E. coli Hsp70/DnaK
Q42380595	Implicit Solvent Model for Million-Atom Atomistic Simulations: Insights into the Organization of 30-nm Chromatin Fiber
Q52653810	Implicit ligand theory for relative binding free energies
Q30367039	Implicit modeling of nonpolar solvation for simulating protein folding and conformational transitions.
Q64063487	Importance of Incorporating Protein Flexibility in Molecule Modeling: A Theoretical Study on Type I NIK Inhibitors
Q41490277	Importance of protein flexibility in ranking inhibitor affinities: modeling the binding mechanisms of piperidine carboxamides as Type I1/2 ALK inhibitors
Q47225930	Importance of protein flexibility on molecular recognition: modeling binding mechanisms of aminopyrazine inhibitors to Nek2.
Q35180754	Improved Generalized Born Solvent Model Parameters for Protein Simulations
Q90126618	Improved Poisson-Boltzmann Methods for High-Performance Computing
Q36335364	Improved coarse-graining of Markov state models via explicit consideration of statistical uncertainty
Q54963827	Improving Docking Performance Using Negative Image-Based Rescoring.
Q36077609	Improving the description of salt bridge strength and geometry in a Generalized Born model
Q33886126	In Silico Elucidation of the Recognition Dynamics of Ubiquitin
Q28820755	In Silico Exploration for Novel Type-I Inhibitors of Tie-2/TEK: The Performance of Different Selection Strategy in Selecting Virtual Screening Candidates
Q90333802	In Silico Screening and Binding Characterization of Small Molecules toward a G-Quadruplex Structure Formed in the Promoter Region of c-MYC Oncogene
Q64064354	In silico identification of genetic mutations conferring resistance to acetohydroxyacid synthase inhibitors: A case study of Kochia scoparia
Q38917669	In silico investigation on the inhibition of Aβ42 aggregation by Aβ40 peptide by potential of mean force study
Q99239350	In-silico prediction of novel drug-target complex of nsp3 of CHIKV through molecular dynamic simulation
Q42908168	Inclusion of Carboxyl Function Inside of Cucurbiturils and its Use in Molecular Switches
Q44909942	Incorporating variable dielectric environments into the generalized Born model
Q35871478	Influence of Chirality of Crizotinib on Its MTH1 Protein Inhibitory Activity: Insight from Molecular Dynamics Simulations and Binding Free Energy Calculations
Q58794868	Influence of various parameters in the replica-exchange molecular dynamics method: Number of replicas, replica-exchange frequency, and thermostat coupling time constant
Q64072952	Inhibition of NLRP3 inflammasome activation by cell-permeable stapled peptides
Q36237626	Inhibition of acetylcholinesterase by two genistein derivatives: kinetic analysis, molecular docking and molecular dynamics simulation
Q46715651	Inhibitory effects and oxidation of 6-methylcoumarin, 7-methylcoumarin and 7-formylcoumarin via human CYP2A6 and its mouse and pig orthologous enzymes
Q34405772	Initial Binding of Ions to the Interhelical Loops of Divalent Ion Transporter CorA: Replica Exchange Molecular Dynamics Simulation Study
Q92926402	Initial Structural Models of the Aβ42 Dimer from Replica Exchange Molecular Dynamics Simulations
Q34350522	Initial conformational changes of human transthyretin under partially denaturing conditions
Q47763550	Insight into Crizotinib Resistance Mechanisms Caused by Three Mutations in ALK Tyrosine Kinase using Free Energy Calculation Approaches
Q30359261	Insight into conformational change for 14-3-3σ protein by molecular dynamics simulation.
Q50866378	Insight into the binding modes and inhibition mechanisms of adamantyl-based 1,3-disubstituted urea inhibitors in the active site of the human soluble epoxide hydrolase
Q87984385	Insight into the interaction mechanism of human SGLT2 with its inhibitors: 3D-QSAR studies, homology modeling, and molecular docking and molecular dynamics simulations
Q50951740	Insight into the key features for ligand binding in Y1230 mutated c-Met kinase domain by molecular dynamics simulations
Q47619234	Insight into the molecular mechanism about lowered dihydrofolate binding affinity to dihydrofolate reductase-like 1 (DHFRL1).
Q49722085	Insight into the molecular mechanism of yeast acetyl-coenzyme A carboxylase mutants F510I, N485G, I69E, E477R, and K73R resistant to soraphen A.
Q51422284	Insights into Structural Properties of Denatured Human Prion 121-230 at Melting Temperature Studied by Replica Exchange Molecular Dynamics
Q28547256	Insights into the Interactions of Fasciola hepatica Cathepsin L3 with a Substrate and Potential Novel Inhibitors through In Silico Approaches
Q48175839	Insights into the Molecular Mechanisms of Alzheimer's and Parkinson's Diseases with Molecular Simulations: Understanding the Roles of Artificial and Pathological Missense Mutations in Intrinsically Disordered Proteins Related to Pathology
Q52565862	Insights into the binding mode of sulphamates and sulphamides to hCA II: crystallographic studies and binding free energy calculations
Q51315203	Insights into the drug resistance induced by the BaDHPS mutations: molecular dynamic simulations and MM/GBSA studies
Q30366178	Insights on the structure and stability of Licanantase: a trimeric acid-stable coiled-coil lipoprotein from Acidithiobacillus thiooxidans.
Q50797726	Interaction mechanism exploration of R-bicalutamide/S-1 with WT/W741L AR using molecular dynamics simulations
Q36538279	Interactions between neuronal fusion proteins explored by molecular dynamics
Q53323897	Interactions of amyloid β peptide 1-40 and cerebrosterol
Q38878454	Interactions of omeprazole-based analogues with cytochrome P450 2C19: a computational study
Q39371272	Interactions of two O-phosphorylresveratrol derivatives with model membranes
Q51723604	Interpolation schemes for peptide rearrangements
Q57214919	Intracellular Pathways Involved in Bone Regeneration Triggered by Recombinant Silk-silica Chimeras
Q40962797	Intrinsically disordered energy landscapes
Q33640094	Intrinsically disordered regions may lower the hydration free energy in proteins: a case study of nudix hydrolase in the bacterium Deinococcus radiodurans
Q90153376	Investigating Conformational Dynamics of Lewis Y Oligosaccharides and Elucidating Blood Group Dependency of Cholera Using Molecular Dynamics
Q38928519	Investigating Substitutions in Antibody-Antigen Complexes Using Molecular Dynamics: A Case Study with Broad-spectrum, Influenza A Antibodies.
Q44856146	Investigating rare events with nonequilibrium work measurements. I. Nonequilibrium transition path probabilities
Q44856151	Investigating rare events with nonequilibrium work measurements. II. Transition and reaction rates
Q41646833	Investigation of the dynamics of the viral immediate-early protein 1 in different conformations and oligomerization states
Q47822146	Investigation on the binding mechanism of loratinib with the c-ros oncogene 1 (ROS1) receptor tyrosine kinase via molecular dynamics simulation and binding free energy calculations.
Q46027361	Is Poisson-Boltzmann theory insufficient for protein folding simulations?
Q91810081	Isoform-specific Inhibition of N-methyl-D-aspartate Receptors by Bile Salts
Q30371226	Iterative assembly of helical proteins by optimal hydrophobic packing.
Q35076388	KECSA-Movable Type Implicit Solvation Model (KMTISM).
Q60925516	KRas4B-PDE6δ complex stabilization by small molecules obtained by virtual screening affects Ras signaling in pancreatic cancer
Q91971816	Key Features Relevant to Select Antigens and TCR From the MHC-Mismatched Repertoire to Treat Cancer
Q90694100	Key residues in TLR4-MD2 tetramer formation identified by free energy simulations
Q91130078	Kinetic Control of Parallel versus Antiparallel Amyloid Aggregation via Shape of the Growing Aggregate
Q42145390	Kinetics of helix unfolding: molecular dynamics simulations with milestoning
Q33392477	Knottin cyclization: impact on structure and dynamics
Q90309006	Ligand Binding Mechanism and Its Relationship with Conformational Changes in Adenine Riboswitch
Q38129629	Ligand Docking Simulations by Generalized-Ensemble Algorithms
Q52371594	Ligand-induced perturbation of the HIF-2α:ARNT dimer dynamics
Q38715315	Loss of tumor suppressor KDM6A amplifies PRC2-regulated transcriptional repression in bladder cancer and can be targeted through inhibition of EZH2.
Q82599858	MM/GBSA and LIE estimates of host–guest affinities: dependence on charges and solvation model
Q99637403	MMGB/SA Consensus Estimate of the Binding Free Energy Between the Novel Coronavirus Spike Protein to the Human ACE2 Receptor
Q35052399	MSCALE: A General Utility for Multiscale Modeling.
Q37712074	Macrocyclized Extended Peptides: Inhibiting the Substrate-Recognition Domain of Tankyrase.
Q36824469	Mapping Conformational Dynamics of Proteins Using Torsional Dynamics Simulations
Q39472349	Measuring the successes and deficiencies of constant pH molecular dynamics: a blind prediction study
Q45154555	Mechanical Probes of SOD1 Predict Systematic Trends in Metal and Dimer Affinity of ALS-Associated Mutants
Q35252505	Mechanism of inhibition of the human sirtuin enzyme SIRT3 by nicotinamide: computational and experimental studies
Q28474948	Mechanism of microRNA-target interaction: molecular dynamics simulations and thermodynamics analysis
Q91404345	Mechanism of synergistic actin filament pointed end depolymerization by cyclase-associated protein and cofilin
Q41215980	Mechanisms for the inhibition of amyloid aggregation by small ligands.
Q64057222	Methionine Oxidation Changes the Mechanism of Aβ Peptide Binding to the DMPC Bilayer
Q64991262	Mg2+ Binding Promotes SLV as a Scaffold in Varkud Satellite Ribozyme SLI-SLV Kissing Loop Junction.
Q47726693	Mimicking Intermolecular Interactions of Tight Protein-Protein Complexes for Small-Molecule Antagonists.
Q90682454	Modeling Electrostatic Force in Protein-Protein Recognition
Q58881156	Modeling Protein–Protein and Protein–Nucleic Acid Interactions: Structure, Thermodynamics, and Kinetics
Q57117169	Modeling and antitumor studies of a modified L-penetratin peptide targeting E2F in lung cancer and prostate cancer
Q41897177	Modeling the assembly of the multiple domains of α-actinin-4 and its role in actin cross-linking
Q92134598	Modeling the binding of diverse ligands within the Ah receptor ligand binding domain
Q50854147	Modeling the interactions between MC2R and ACTH models from human
Q90127054	Molecular Dynamics Ensemble Refinement of Intrinsically Disordered Peptides According to Deconvoluted Spectra from Circular Dichroism
Q46326598	Molecular Dynamics Simulation Study on the Molecular Structures of the Amylin Fibril Models
Q39685426	Molecular Dynamics Simulation and Free Energy Calculation Studies of the Binding Mechanism of Allosteric Inhibitors with p38α MAP Kinase
Q84856812	Molecular Dynamics Simulation of Free and Forced BSA Adsorption on a Hydrophobic Graphite Surface
Q62751097	Molecular Dynamics Simulations Revealed the Regulation of Ligands to the Interactions between Androgen Receptor and Its Coactivator
Q50790141	Molecular Dynamics Simulations to Investigate the Binding Mode of the Natural Product Liphagal with Phosphoinositide 3-Kinase α.
Q51144561	Molecular Dynamics Studies on the Enzalutamide Resistance Mechanisms Induced by Androgen Receptor Mutations
Q94564580	Molecular Mechanism of Selective Binding of NMS-P118 to PARP-1 and PARP-2: A Computational Perspective
Q27680598	Molecular Mechanisms of Inhibition of Influenza by Surfactant Protein D Revealed by Large-Scale Molecular Dynamics Simulation
Q42377188	Molecular Mechanisms of the Binding and Specificity of Streptococcus Pneumoniae Sortase C Enzymes for Pilin Subunits
Q49033366	Molecular Modeling Studies of 11β-Hydroxysteroid Dehydrogenase Type 1 Inhibitors through Receptor-Based 3D-QSAR and Molecular Dynamics Simulations
Q92460458	Molecular Modeling of ALK L1198F and/or G1202R Mutations to Determine Differential Crizotinib Sensitivity
Q47362097	Molecular Modeling of Multidrug Properties of Resistance Nodulation Division (RND) Transporters.
Q40230831	Molecular Modeling on Berberine Derivatives toward BuChE: An Integrated Study with Quantitative Structure-Activity Relationships Models, Molecular Docking, and Molecular Dynamics Simulations
Q90484517	Molecular Simulation of Oncostatin M and Receptor (OSM-OSMR) Interaction as a Potential Therapeutic Target for Inflammatory Bowel Disease
Q46480930	Molecular Simulations Bring New Insights into Protoporphyrinogen IX Oxidase/Protoporphyrinogen IX Interaction Modes
Q28485296	Molecular determinants of epidermal growth factor binding: a molecular dynamics study
Q47761027	Molecular docking and molecular dynamics simulations of fumarate hydratase and its mutant H235N complexed with pyromellitic acid and citrate
Q53479485	Molecular docking and molecular dynamics studies on the structure-activity relationship of fluoroquinolone for the HERG channel
Q30375271	Molecular dynamics analysis of antibody recognition and escape by human H1N1 influenza hemagglutinin.
Q34222040	Molecular dynamics analysis of apolipoprotein-D-lipid hydroperoxide interactions: mechanism for selective oxidation of Met-93.
Q85435288	Molecular dynamics and free energy studies of chirality specificity effects on aminobenzo[a]quinolizine inhibitors binding to DPP-IV
Q84993045	Molecular dynamics and free energy studies on Aurora kinase A and its mutant bound with MLN8054: insight into molecular mechanism of subtype selectivity
Q38691180	Molecular dynamics investigations of membrane-bound CYP2C19 polymorphisms reveal distinct mechanisms for peripheral variants by long-range effects on the enzymatic activity.
Q42138585	Molecular dynamics of ribosomal elongation factors G and Tu.
Q28486718	Molecular dynamics reveal binding mode of glutathionylspermidine by trypanothione synthetase
Q43607840	Molecular dynamics simulation indicating cold denaturation of β-hairpins
Q28482621	Molecular dynamics simulation of the complex PBP-2x with drug cefuroxime to explore the drug resistance mechanism of Streptococcus suis R61
Q46367449	Molecular dynamics simulation studies of the structural response of an isolated Aβ1-42 monomer localized in the vicinity of the hydrophilic TiO 2 surface
Q41909739	Molecular dynamics simulations and functional characterization of the interactions of the PAR2 ectodomain with factor VIIa
Q26772040	Molecular dynamics simulations of biological membranes and membrane proteins using enhanced conformational sampling algorithms
Q47625995	Molecular dynamics simulations of β2-microglobulin interaction with hydrophobic surfaces.
Q30399511	Molecular dynamics simulations on networks of heparin and collagen.
Q48451660	Molecular imaging of EGFR kinase activity in tumors with 124I-labeled small molecular tracer and positron emission tomography.
Q39013172	Molecular mechanical properties of short-sequence peptide enzyme mimics
Q51325445	Molecular mechanism of R-bicalutamide switching from androgen receptor antagonist to agonist induced by amino acid mutations using molecular dynamics simulations and free energy calculation
Q42014890	Molecular modeling of Bt Cry1Ac (DI–DII)–ASAL (Allium sativum lectin)–fusion protein and its interaction with aminopeptidase N (APN) receptor of Manduca sexta
Q38336095	Molecular modeling of nucleic Acid structure: electrostatics and solvation
Q38326721	Molecular modeling of nucleic Acid structure: setup and analysis
Q81131493	Molecular modeling of nucleic acid structure: electrostatics and solvation
Q81131476	Molecular modeling of nucleic acid structure: setup and analysis
Q64090194	Molecular modeling simulation studies reveal new potential inhibitors against HPV E6 protein
Q50711550	Molecular modeling studies to characterize N-phenylpyrimidin-2-amine selectivity for CDK2 and CDK4 through 3D-QSAR and molecular dynamics simulations
Q31153312	Molecular modeling study on the allosteric inhibition mechanism of HIV-1 integrase by LEDGF/p75 binding site inhibitors
Q40935601	Molecular modeling study on the drug resistance mechanism of NS5B polymerase to TMC647055.
Q35515481	Molecular modelling studies of sirtuin 2 inhibitors using three-dimensional structure-activity relationship analysis and molecular dynamics simulations
Q33758074	Molecular recognition in a diverse set of protein-ligand interactions studied with molecular dynamics simulations and end-point free energy calculations
Q33862760	Molecular recognition of H3/H4 histone tails by the tudor domains of JMJD2A: a comparative molecular dynamics simulations study
Q24631041	Molecular simulation of ab initio protein folding for a millisecond folder NTL9(1-39)
Q54234353	Molecular simulation studies on the binding selectivity of 2-anilino-4-(thiazol-5-yl)-pyrimidines in complexes with CDK2 and CDK7.
Q37486587	Monitoring the Folding of Trp-Cage Peptide by Two-Dimensional Infrared (2DIR) Spectroscopy
Q44321204	MuSTAR MD: multi-scale sampling using temperature accelerated and replica exchange molecular dynamics.
Q33684624	Multi-scale characterization of the energy landscape of proteins with application to the C3D/Efb-C complex
Q34217831	Multicanonical Molecular Dynamics Simulations of the N-terminal Domain of Protein L9.
Q48043566	Multifunnel Landscape of the Fold-Switching Protein RfaH-CTD.
Q36540017	Multiscale methods for computational RNA enzymology.
Q30651045	Multisite phosphorylation of the NDC80 complex gradually tunes its microtubule-binding affinity
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
Q59799165	Nanoribbons self-assembled from short peptides demonstrate the formation of polar zippers between β-sheets
Q35013460	New compstatin peptides containing N-terminal extensions and non-natural amino acids exhibit potent complement inhibition and improved solubility characteristics
Q52610195	New insights on repellent recognition by Anopheles gambiae odorant-binding protein 1.
Q47939175	Nicotine-modulated subunit stoichiometry affects stability and trafficking of α3β4 nicotinic receptor.
Q37146653	Nitric oxide reactivity with globins as investigated through computer simulation.
Q28542983	Novel inhibitors induce large conformational changes of GAB1 pleckstrin homology domain and kill breast cancer cells
Q42186848	Novel theoretically designed HIV-1 non-nucleoside reverse transcriptase inhibitors derived from nevirapine
Q35974266	Nucleotide-dependent mechanism of Get3 as elucidated from free energy calculations
Q34978174	Observation of Two Families of Folding Pathways of BBL
Q37655137	Of mice and men: Dissecting the interaction between Listeria monocytogenes Internalin A and E-cadherin.
Q42542841	On the Dielectric Boundary in Poisson-Boltzmann Calculations
Q33761266	On the origins of the weak folding cooperativity of a designed ββα ultrafast protein FSD-1.
Q50622139	On the use of mass scaling for stable and efficient simulated tempering with molecular dynamics
Q30415382	OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation
Q64230078	Osthole protects against Ang II-induced endotheliocyte death by targeting NF-κB pathway and Keap-1/Nrf2 pathway
Q48193574	Out-of-Register Aβ42 Assemblies as Models for Neurotoxic Oligomers and Fibrils
Q92108061	Oxidation State Dependent Conformational Changes of HMGB1 Regulate the Formation of the CXCL12/HMGB1 Heterocomplex
Q38765858	PDEδ Binding to Ras Isoforms Provides a Route to Proper Membrane Localization.
Q51733078	Pairwise decomposition of an MMGBSA energy function for computational protein design
Q35569847	Parallel Generalized Born Implicit Solvent Calculations with NAMD.
Q36711952	Parallelization and improvements of the generalized born model with a simple sWitching function for modern graphics processors
Q30986053	Parameterization of an effective potential for protein-ligand binding from host-guest affinity data.
Q41144268	Parameterization of the Hamiltonian Dielectric Solvent (HADES) Reaction-Field Method for the Solvation Free Energies of Amino Acid Side-Chain Analogs
Q47361639	Peptide modulators of Rac1/Tiam1 protein-protein interaction: An alternative approach for cardiovascular diseases.
Q33562598	Peptide probes derived from pertuzumab by molecular dynamics modeling for HER2 positive tumor imaging
Q53078387	Peptoid conformational free energy landscapes from implicit-solvent molecular simulations in AMBER.
Q47797655	Performance of multiple docking and refinement methods in the pose prediction D3R prospective Grand Challenge 2016.
Q54477930	Pharmacophore based 3D-QSAR modeling and free energy analysis of VEGFR-2 inhibitors
Q51406832	Phosphorylation of KLHL3 at serine 433 impairs its interaction with the acidic motif of WNK4: a molecular dynamics study
Q38072041	Poisson-Boltzmann Calculations: van der Waals or Molecular Surface?
Q58881112	Poisson-Boltzmann Calculations: van der Waals or Molecular Surface?
Q35776163	Polar Desolvation and Position 226 of Pancreatic and Neutrophil Elastases Are Crucial to their Affinity for the Kunitz-Type Inhibitors ShPI-1 and ShPI-1/K13L
Q38630201	Polarizable Atomic Multipole Solutes in a Generalized Kirkwood Continuum
Q50560983	Positive cooperative regulation of double binding sites for human acetylcholinesterase
Q41021675	Potential inhibitory effect of indolizine derivatives on the two enzymes: nicotinamide phosphoribosyltransferase and beta lactamase, a molecular dynamics study
Q92718601	Pre-folded structures govern folding pathways of human telomeric G-quadruplexes
Q38764353	Predicting binding modes of reversible peptide-based inhibitors of falcipain-2 consistent with structure-activity relationships.
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P356	DOI	10.1002/PROT.20033
P3181	OpenCitations bibliographic resource ID	546884
P698	PubMed publication ID	15048829
P5875	ResearchGate publication ID	8651735

P2093	author name string	Case DA
		Bashford D
		Onufriev A
P433	issue	2
P407	language of work or name	English	Q1860
P304	page(s)	383-94
P577	publication date	2004-05-01
P1433	published in	Proteins	Q7251514
P1476	title	Exploring protein native states and large-scale conformational changes with a modified generalized born model
P478	volume	55

Exploring protein native states and large-scale conformational changes with a modified generalized born model

scientific article (publication date: May 2004)

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