| review article | Q7318358 |
| scholarly article | Q13442814 |
| P50 | author | J. Andrew McCammon | Q6104601 |
| P2093 | author name string | Stewart A Adcock | |
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| Protein folding-simulation | Q36472815 | ||
| On the evaluation and optimization of protein X-ray structures for pKa calculations | Q36559778 | ||
| Protein hydration elucidated by molecular dynamics simulation | Q36574680 | ||
| Studying the roles of W86, E202, and Y337 in binding of acetylcholine to acetylcholinesterase using a combined molecular dynamics and multiple docking approach | Q36631467 | ||
| Molecular dynamics: deciphering the data | Q36819901 | ||
| A naphthyridine carboxamide provides evidence for discordant resistance between mechanistically identical inhibitors of HIV-1 integrase | Q37388364 | ||
| Extending the capabilities of targeted molecular dynamics: simulation of a large conformational transition in plasminogen activator inhibitor 1. | Q38271704 | ||
| Filtering molecular dynamics trajectories to reveal low-frequency collective motions: phospholipase A2. | Q39276842 | ||
| Structure, interaction, dynamics and solvent effects on the DNA-EcoRI complex in aqueous solution from molecular dynamics simulation | Q40150434 | ||
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| Prediction of the binding free energies of new TIBO-like HIV-1 reverse transcriptase inhibitors using a combination of PROFEC, PB/SA, CMC/MD, and free energy calculations | Q41612429 | ||
| Flexible ligand docking: a multistep strategy approach | Q41673303 | ||
| Use of MM-PB/SA in estimating the free energies of proteins: application to native, intermediates, and unfolded villin headpiece | Q41736263 | ||
| Understanding the determinants of stability and folding of small globular proteins from their energetics | Q42256313 | ||
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| Contributions to the binding free energy of ligands to avidin and streptavidin. | Q43947466 | ||
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| Studying enzyme binding specificity in acetylcholinesterase using a combined molecular dynamics and multiple docking approach | Q44054097 | ||
| Carbohydrate solution simulations: producing a force field with experimentally consistent primary alcohol rotational frequencies and populations | Q44124575 | ||
| Derivation of class II force fields. VIII. Derivation of a general quantum mechanical force field for organic compounds | Q44239882 | ||
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| Discovery of a novel binding trench in HIV integrase. | Q34546744 | ||
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| Protein flexibility is an important component of structure-based drug discovery. | Q34673812 | ||
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| Long time dynamics of complex systems | Q34691143 | ||
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| Molecular dynamics applied to nucleic acids | Q34691218 | ||
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| Protein simulation and drug design | Q35590732 | ||
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| Binding affinity prediction with different force fields: examination of the linear interaction energy method | Q33202843 | ||
| Molecular dynamics simulations of biomolecules: long-range electrostatic effects | Q33689931 | ||
| Minimization of polypeptide energy. 8. Application of the deflation technique to a dipeptide | Q33816925 | ||
| Accommodating protein flexibility in computational drug design | Q33825095 | ||
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| The statistical-thermodynamic basis for computation of binding affinities: a critical review | Q33915676 | ||
| Anisotropy of fluctuation dynamics of proteins with an elastic network model | Q33931550 | ||
| Steered molecular dynamics and mechanical functions of proteins | Q33942097 | ||
| Simulations of ion channels--watching ions and water move | Q33984506 | ||
| Generalized born models of macromolecular solvation effects | Q34059768 | ||
| Molecular dynamics simulation of nucleic acids | Q34059796 | ||
| Energetics of glycerol conduction through aquaglyceroporin GlpF. | Q34067362 | ||
| On the calculation of absolute macromolecular binding free energies | Q34074487 | ||
| Implicit Solvation Models: Equilibria, Structure, Spectra, and Dynamics | Q34114477 | ||
| Transition path sampling: throwing ropes over rough mountain passes, in the dark. | Q34125120 | ||
| Sensitive force technique to probe molecular adhesion and structural linkages at biological interfaces | Q34129714 | ||
| Molecular dynamics studies on the HIV-1 integrase catalytic domain | Q34170581 | ||
| Molecular dynamics studies of the wild-type and double mutant HIV-1 integrase complexed with the 5CITEP inhibitor: mechanism for inhibition and drug resistance | Q34180538 | ||
| Molecular dynamics simulations of peptides and proteins with amplified collective motions | Q34181379 | ||
| Mechanisms of selectivity in channels and enzymes studied with interactive molecular dynamics | Q34181800 | ||
| Optical trapping and manipulation of viruses and bacteria | Q34183243 | ||
| Revisiting free energy calculations: a theoretical connection to MM/PBSA and direct calculation of the association free energy | Q34184435 | ||
| Polarizable force fields | Q34215898 | ||
| Macromolecular electrostatics: continuum models and their growing pains | Q34215908 | ||
| Probing the relation between force--lifetime--and chemistry in single molecular bonds | Q34243206 | ||
| Biomolecular simulations: recent developments in force fields, simulations of enzyme catalysis, protein-ligand, protein-protein, and protein-nucleic acid noncovalent interactions | Q34243228 | ||
| CHARMM fluctuating charge force field for proteins: I parameterization and application to bulk organic liquid simulations. | Q34278687 | ||
| Generalized-ensemble algorithms for molecular simulations of biopolymers | Q34309528 | ||
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| CHARMM fluctuating charge force field for proteins: II protein/solvent properties from molecular dynamics simulations using a nonadditive electrostatic model. | Q34329900 | ||
| Empirical force fields for biological macromolecules: overview and issues. | Q34334583 | ||
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| BioSimGrid: towards a worldwide repository for biomolecular simulations | Q45144903 | ||
| Accelerated molecular dynamics: a promising and efficient simulation method for biomolecules | Q46058456 | ||
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| Interactive essential dynamics | Q46159218 | ||
| The application of three approximate free energy calculations methods to structure based ligand design: trypsin and its complex with inhibitors | Q46164687 | ||
| Equilibrium information from nonequilibrium measurements in an experimental test of Jarzynski's equality | Q46248058 | ||
| Multiple time step diffusive Langevin dynamics for proteins | Q46356926 | ||
| Accelerated Poisson-Boltzmann calculations for static and dynamic systems | Q46543722 | ||
| Free energy surfaces of beta-hairpin and alpha-helical peptides generated by replica exchange molecular dynamics with the AGBNP implicit solvent model | Q47307353 | ||
| Time-trimming tricks for dynamic simulations: splitting force updates to reduce computational work | Q47617892 | ||
| Cooperative fluctuations and subunit communication in tryptophan synthase | Q47623777 | ||
| Collective motions in HIV-1 reverse transcriptase: examination of flexibility and enzyme function. | Q47624236 | ||
| Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential | Q47628195 | ||
| Protein hydration density: theory, simulations and crystallography | Q47959626 | ||
| Rate constants for diffusive processes by partial path sampling. | Q51636084 | ||
| Solvation forces on biomolecular structures: a comparison of explicit solvent and Poisson-Boltzmann models. | Q51643871 | ||
| Automatic domain decomposition of proteins by a Gaussian Network Model. | Q51986886 | ||
| Prediction of pKa shifts in proteins using a combination of molecular mechanical and continuum solvent calculations. | Q51989385 | ||
| Computing time scales from reaction coordinates by milestoning. | Q51993371 | ||
| An alternative multipolar expansion for intermolecular potential functions. | Q51993561 | ||
| Exploring the natural conformational changes of the C-terminal domain of calmodulin. | Q52031199 | ||
| Simulating proteins at constant pH: An approach combining molecular dynamics and Monte Carlo simulation. | Q52040919 | ||
| Multiple grid methods for classical molecular dynamics. | Q52043059 | ||
| MCSS functionality maps for a flexible protein. | Q52082500 | ||
| Docking of flexible ligands to flexible receptors in solution by molecular dynamics simulation. | Q52216410 | ||
| Computer simulations with explicit solvent: recent progress in the thermodynamic decomposition of free energies and in modeling electrostatic effects. | Q52224995 | ||
| Molecular dynamics simulation of the docking of substrates to proteins. | Q52375019 | ||
| Protein electrostatics: rapid multigrid-based Newton algorithm for solution of the full nonlinear Poisson-Boltzmann equation. | Q52376681 | ||
| A structure refinement method based on molecular dynamics in four spatial dimensions. | Q52386873 | ||
| Active site dynamics in protein molecules: a stochastic boundary molecular-dynamics approach. | Q52671795 | ||
| Ordered water and ligand mobility in the HIV-1 integrase-5CITEP complex: a molecular dynamics study. | Q53886381 | ||
| Zur Quantentheorie der Molekeln | Q54152578 | ||
| Structural basis for cooperative DNA binding by CAP and lac repressor. | Q54512349 | ||
| AGBNP: an analytic implicit solvent model suitable for molecular dynamics simulations and high-resolution modeling. | Q54640063 | ||
| Large Amplitude Elastic Motions in Proteins from a Single-Parameter, Atomic Analysis | Q56688821 | ||
| Poisson–Boltzmann Methods for Biomolecular Electrostatics | Q56934551 | ||
| Prediction of protein conformational freedom from distance constraints | Q57754185 | ||
| Principles of docking: An overview of search algorithms and a guide to scoring functions | Q57808017 | ||
| Conformational sampling using high-temperature molecular dynamics | Q68545089 | ||
| Computational studies of ligand diffusion in globins: I. Leghemoglobin | Q70216505 | ||
| A method for including protein flexibility in protein-ligand docking: improving tools for database mining and virtual screening | Q73047696 | ||
| Free energy grids: a practical qualitative application of free energy perturbation to ligand design using the OWFEG method | Q73138375 | ||
| Simulation of protein conformational freedom as a function of pH: constant-pH molecular dynamics using implicit titration | Q73319277 | ||
| Improved scoring of ligand-protein interactions using OWFEG free energy grids | Q73423412 | ||
| Computer simulations of protein folding by targeted molecular dynamics | Q73594418 | ||
| P433 | issue | 5 | |
| P304 | page(s) | 1589-1615 | |
| P577 | publication date | 2006-05-01 | |
| P1433 | published in | Chemical Reviews | Q900502 |
| P1476 | title | Molecular dynamics: survey of methods for simulating the activity of proteins | |
| P478 | volume | 106 |
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| Q40081462 | Biophysical and Computational Studies of the vCCI:vMIP-II Complex |
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| Q58454496 | Chapter 2 Electrostatics in Biomolecular Simulations: Where Are We Now and Where Are We Heading? |
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| Q34186621 | Combining weak affinity chromatography, NMR spectroscopy and molecular simulations in carbohydrate-lysozyme interaction studies. |
| Q36388154 | Comparative molecular dynamics analysis of tapasin-dependent and -independent MHC class I alleles |
| Q30386769 | Comparing pharmacophore models derived from crystal structures and from molecular dynamics simulations |
| Q37149481 | Comparison of dynamics of wildtype and V94M human UDP-galactose 4-epimerase-A computational perspective on severe epimerase-deficiency galactosemia. |
| Q40384429 | Complexation of short ds RNA/DNA oligonucleotides with Gemini micelles: a time resolved SAXS and computational study. |
| Q30489757 | Computation of conformational transitions in proteins by virtual atom molecular mechanics as validated in application to adenylate kinase |
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| Q26777448 | Computational drug design strategies applied to the modelling of human immunodeficiency virus-1 reverse transcriptase inhibitors |
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| Q37375373 | Computational evaluation of protein-small molecule binding. |
| Q42858930 | Computational modeling of phosphotransfer complexes in two-component signaling |
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| Q90044975 | Computational study of paroxetine-like inhibitors reveals new molecular insight to inhibit GRK2 with selectivity over ROCK1 |
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| Q84749816 | Conformational dynamics of threonine 195 and the S1 subsite in functional trypsin variants |
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| Q50943651 | Experimental and theoretical studies of cadmium ions absorption by a new reduced recombinant defensin. |
| Q38821099 | Exploiting computationally derived out-of-the-box protein conformations for drug design. |
| Q41856020 | Exploiting conformational dynamics in drug discovery: design of C-terminal inhibitors of Hsp90 with improved activities |
| Q36362316 | Exploring Valleys without Climbing Every Peak: More Efficient and Forgiving Metabasin Metadynamics via Robust On-the-Fly Bias Domain Restriction |
| Q38033254 | Exploring the mechanism of a regulatory SNP of KLK3 by molecular dynamics simulation |
| Q27001129 | Exploring the role of receptor flexibility in structure-based drug discovery |
| Q33735791 | Finding semirigid domains in biomolecules by clustering pair-distance variations |
| Q84629463 | Folding dynamics of a small protein at room temperature via simulated coherent two-dimensional infrared spectroscopy |
| Q38182184 | Foundations for modeling the dynamics of gene regulatory networks: a multilevel-perspective review |
| Q42161091 | Free Energy Calculations using a Swarm-Enhanced Sampling Molecular Dynamics Approach. |
| Q28652087 | Functional loop dynamics of the streptavidin-biotin complex |
| Q39419666 | G-Protein coupled receptors: answers from simulations |
| Q47348724 | GPCRs: What Can We Learn from Molecular Dynamics Simulations? |
| Q30484994 | Gating at both ends and breathing in the middle: conformational dynamics of TolC. |
| Q48012048 | Generalized essential energy space random walks to more effectively accelerate solute sampling in aqueous environment |
| Q33852251 | Geometric analysis of alloreactive HLA α-helices. |
| Q34415966 | GneimoSim: a modular internal coordinates molecular dynamics simulation package. |
| Q45909863 | Grcarma: A fully automated task-oriented interface for the analysis of molecular dynamics trajectories. |
| Q38469746 | Heat-shock protein 90 (Hsp90) as anticancer target for drug discovery: an ample computational perspective |
| Q46062870 | Homology model adjustment and ligand screening with a pseudoreceptor of the human histamine H4 receptor |
| Q37596407 | Identification of an L-phenylalanine binding site enhancing the cooperative responses of the calcium-sensing receptor to calcium. |
| Q30387121 | Implementation of molecular dynamics and its extensions with the coarse-grained UNRES force field on massively parallel systems; towards millisecond-scale simulations of protein structure, dynamics, and thermodynamics. |
| Q42380595 | Implicit Solvent Model for Million-Atom Atomistic Simulations: Insights into the Organization of 30-nm Chromatin Fiber |
| Q51424938 | In Silico Methods for Analyzing Mutagenesis Targets. |
| Q90012937 | In Vivo Activities and In Silico Study of Jackfruit Seeds (Artocarpus heterophyllus Lam.) on the Reduction of Blood Sugar Levels of Gestational Diabetes Rate Induced by Streptozotocin |
| Q35310313 | In silico modification of oseltamivir as neuraminidase inhibitor of influenza A virus subtype H1N1. |
| Q34175711 | Including receptor flexibility and induced fit effects into the design of MMP-2 inhibitors |
| Q37159181 | Independent-Trajectories Thermodynamic-Integration Free-Energy Changes for Biomolecular Systems: Determinants of H5N1 Avian Influenza Virus Neuraminidase Inhibition by Peramivir |
| Q37577586 | Individual-based modelling: an essential tool for microbiology |
| Q48237854 | Insights into the structural function of the complex of HIV-1 protease with TMC-126: molecular dynamics simulations and free-energy calculations |
| Q36649931 | Integrating molecular dynamics simulations with chemical probing experiments using SHAPE-FIT. |
| Q30369903 | Internal coordinate molecular dynamics: a foundation for multiscale dynamics |
| Q30375748 | Intra-protein hydrogen bonding is dynamically stabilized by electronic polarization. |
| Q89910220 | Investigation of molecular aggregation mechanism of glipizide/cyclodextrin complexation by combined experimental and molecular modeling approaches |
| Q42237069 | Investigation on the mechanism for the binding and drug resistance of wild type and mutations of G86 residue in HIV-1 protease complexed with Darunavir by molecular dynamic simulation and free energy calculation |
| Q36809572 | Key intermolecular interactions in the E. coli 70S ribosome revealed by coarse-grained analysis |
| Q37728989 | L1198F Mutation Resensitizes Crizotinib to ALK by Altering the Conformation of Inhibitor and ATP Binding Sites |
| Q33837160 | Large conformational changes in proteins: signaling and other functions |
| Q35208080 | LipidWrapper: an algorithm for generating large-scale membrane models of arbitrary geometry |
| Q36824469 | Mapping conformational dynamics of proteins using torsional dynamics simulations |
| Q27327268 | Mapping paratope on antithrombotic antibody 6B4 to epitope on platelet glycoprotein Ibalpha via molecular dynamic simulations |
| Q34054370 | Mapping the druggable allosteric space of G-protein coupled receptors: a fragment-based molecular dynamics approach |
| Q34776635 | Mathematical models in biology: from molecules to life |
| Q37265691 | Mechanism of interaction between the general anesthetic halothane and a model ion channel protein, III: Molecular dynamics simulation incorporating a cyanophenylalanine spectroscopic probe |
| Q42142586 | Mechanism of mRNA-STAR domain interaction: Molecular dynamics simulations of Mammalian Quaking STAR protein |
| Q47158852 | Mechanistic Insights into the Reaction of Chlorination of Tryptophan Catalyzed by Tryptophan 7-Halogenase |
| Q37118422 | Mechanistic insight into the role of transition-state stabilization in cyclophilin A. |
| Q48310540 | Membrane negative curvature induced by a hybrid peptide from pediocin PA-1 and plantaricin 149 as revealed by atomistic molecular dynamics simulations. |
| Q47617911 | Migration of PIP2 on KCNQ2 Surface Revealed by Molecular Dynamics Simulations |
| Q34306952 | Modeling DNA polymerase μ motions: subtle transitions before chemistry |
| Q28817434 | Modeling Electronic Polarizability Changes in the Course of a Magnesium Ion Water Ligand Exchange Process |
| Q34097303 | Modelling zwitterions in solution: 3-fluoro-γ-aminobutyric acid (3F-GABA). |
| Q51565431 | Molecular Docking, Molecular Dynamics Simulations, Computational Screening to Design Quorum Sensing Inhibitors Targeting LuxP of Vibrio harveyi and Its Biological Evaluation. |
| Q51603766 | Molecular Dynamics Simulations of G Protein-Coupled Receptors. |
| Q42674180 | Molecular cloning, relative expression, and structural analysis of pattern recognition molecule β-glucan binding protein from mangrove crab Episesarma tetragonum |
| Q30483365 | Molecular dynamics of a kappaB DNA element: base flipping via cross-strand intercalative stacking in a microsecond-scale simulation |
| Q36104304 | Molecular dynamics simulation in virus research |
| Q43263551 | Molecular dynamics simulation of a carboxy murine neuroglobin mutated on the proximal side: heme displacement and concomitant rearrangement in loop regions |
| Q30389890 | Molecular dynamics simulation of oseltamivir resistance in neuraminidase of avian influenza H5N1 virus |
| Q34061019 | Molecular dynamics simulations and drug discovery |
| Q47400742 | Molecular dynamics simulations and novel drug discovery |
| Q51091171 | Molecular dynamics simulations elucidate conformational selection and induced fit mechanisms in the binding of PD-1 and PD-L1. |
| Q35963402 | Molecular dynamics simulations reveal a disorder-to-order transition on phosphorylation of smooth muscle myosin. |
| Q30383681 | Molecular dynamics study of prolyl oligopeptidase with inhibitor in binding cavity. |
| Q30374261 | Molecular dynamics study of the structure, flexibility and dynamics of thermostable l1 lipase at high temperatures. |
| Q91994595 | Multi-Target β-Protease Inhibitors from Andrographis paniculata: In Silico and In Vitro Studies |
| Q30488313 | Multiple pathways guide oxygen diffusion into flavoenzyme active sites |
| Q37391214 | Multiscale generalized born modeling of ligand binding energies for virtual database screening. |
| Q35123059 | Multiscale simulations suggest a mechanism for integrin inside-out activation |
| Q36140604 | Mutations as trapdoors to two competing native conformations of the Rop-dimer |
| Q34053706 | NNScore 2.0: a neural-network receptor-ligand scoring function |
| Q35163073 | Non-bisphosphonate inhibitors of isoprenoid biosynthesis identified via computer-aided drug design. |
| Q42650824 | Normal mode-guided transition pathway generation in proteins. |
| Q30367220 | Novel druggable hot spots in avian influenza neuraminidase H5N1 revealed by computational solvent mapping of a reduced and representative receptor ensemble. |
| Q47446145 | Novel quinazolinone-based 2,4-thiazolidinedione-3-acetic acid derivatives as potent aldose reductase inhibitors. |
| Q39162913 | Optimized parameter selection reveals trends in Markov state models for protein folding. |
| Q38818618 | Overview of the SAMPL5 host-guest challenge: Are we doing better? |
| Q39050030 | Partially Assembled Nucleosome Structures at Atomic Detail |
| Q38189746 | Physicochemical bases for protein folding, dynamics, and protein-ligand binding |
| Q37665888 | Physiologically based pharmacokinetic models: integration of in silico approaches with micro cell culture analogues |
| Q42032808 | Polymorphism of the epidermal growth factor receptor extracellular ligand binding domain: the dimer interface depends on domain stabilization |
| Q34060024 | Predicting protein ligand binding motions with the conformation explorer |
| Q93202753 | Prospects of multitarget drug designing strategies by linking molecular docking and molecular dynamics to explore the protein-ligand recognition process |
| Q35661992 | Protecting High Energy Barriers: A New Equation to Regulate Boost Energy in Accelerated Molecular Dynamics Simulations |
| Q30478048 | Protein complex formation by acetylcholinesterase and the neurotoxin fasciculin-2 appears to involve an induced-fit mechanism |
| Q38167555 | Protein disulfide engineering. |
| Q34093006 | Protein dynamics via computational microscope |
| Q37785587 | Protein functional landscapes, dynamics, allostery: a tortuous path towards a universal theoretical framework. |
| Q47589572 | Protein segments with conformationally restricted amino acids can control supramolecular organization at the nanoscale |
| Q50521605 | Protein stability and dynamics influenced by ligands in extremophilic complexes - a molecular dynamics investigation. |
| Q33966053 | Protonation/deprotonation effects on the stability of the Trp-cage miniprotein |
| Q30039761 | Pyrone-Based Inhibitors of Metalloproteinase Types 2 and 3 May Work as Conformation-Selective Inhibitors |
| Q28755650 | R.E.DD.B.: a database for RESP and ESP atomic charges, and force field libraries |
| Q47396971 | Rational and Semirational Protein Design |
| Q34359877 | Recent advances in computational predictions of NMR parameters for the structure elucidation of carbohydrates: methods and limitations. |
| Q91313806 | Recent studies of docking and molecular dynamics simulation for liquid-phase enantioseparations |
| Q44117527 | Reconstructing the free-energy landscape of Met-enkephalin using dihedral principal component analysis and well-tempered metadynamics |
| Q45345552 | Refinement of the application of the GROMOS 54A7 force field to β-peptides |
| Q35080674 | Revealing the favorable dissociation pathway of type II kinase inhibitors via enhanced sampling simulations and two-end-state calculations |
| Q31154801 | Reversible folding simulation by hybrid Hamiltonian replica exchange |
| Q34211343 | Role of dynamics in the autoinhibition and activation of the exchange protein directly activated by cyclic AMP (EPAC) |
| Q34918623 | SIMS: a hybrid method for rapid conformational analysis. |
| Q58048725 | Sampling large conformational transitions: adenylate kinase as a testing ground |
| Q46685715 | Sampling of slow diffusive conformational transitions with accelerated molecular dynamics |
| Q51757892 | Selecting Conformational Ensembles Using Residual Electron and Anomalous Density (READ). |
| Q46686456 | Sensitivity of peptide conformational dynamics on clustering of a classical molecular dynamics trajectory |
| Q30366106 | Shock Wave-Induced Damage of a Protein by Void Collapse |
| Q33374550 | Side-chain conformational space analysis (SCSA): a multi conformation-based QSAR approach for modeling and prediction of protein-peptide binding affinities |
| Q41997204 | Side-chain hydrophobicity and the stability of Aβ₁₆₋₂₂ aggregates |
| Q30393985 | Simulations of a protein crystal with a high resolution X-ray structure: evaluation of force fields and water models |
| Q48050340 | Simultaneous NMR characterisation of multiple minima in the free energy landscape of an RNA UUCG tetraloop |
| Q47580994 | Single-pass incremental force updates for adaptively restrained molecular dynamics. |
| Q84405819 | Small molecules containing hetero-bicyclic ring systems compete with UDP-Glc for binding to WaaG glycosyltransferase |
| Q39919628 | Spatiotemporal multistage consensus clustering in molecular dynamics studies of large proteins. |
| Q35794917 | Statistical mechanics and molecular dynamics in evaluating thermodynamic properties of biomolecular recognition |
| Q90332751 | Structural Features and Ligand Selectivity for 10 Intermediates in the Activation Process of β2-Adrenergic Receptor |
| Q97521184 | Structural change of retinoic-acid receptor-related orphan receptor induced by binding of inverse-agonist: Molecular dynamics and ab initio molecular orbital simulations |
| Q57063517 | Structure and Dynamics of tRNA Containing Core Substitutions |
| Q41930155 | Structure based Virtual Screening toward the discovery of novel inhibitors for impeding the protein-protein interaction between HIV-1 integrase and human lens epithelium-derived growth factor (LEDGF/p75). |
| Q30480228 | Structure refinement of the OpcA adhesin using molecular dynamics |
| Q37624622 | Structure, mechanism, and dynamics of UDP-galactopyranose mutase |
| Q33348995 | Structures of human proteinase 3 and neutrophil elastase--so similar yet so different |
| Q42582380 | Studying interactions by molecular dynamics simulations at high concentration |
| Q30481294 | Substrate binding and formation of an occluded state in the leucine transporter |
| Q24336071 | Substrate recognition by complement convertases revealed in the C5-cobra venom factor complex |
| Q28756561 | The N-clasp of human DNA polymerase kappa promotes blockage or error-free bypass of adenine- or guanine-benzo[a]pyrenyl lesions |
| Q28483218 | The lipopolysaccharide from Capnocytophaga canimorsus reveals an unexpected role of the core-oligosaccharide in MD-2 binding |
| Q30497423 | The nucleotide addition cycle of RNA polymerase is controlled by two molecular hinges in the Bridge Helix domain |
| Q33638338 | The role of nonbonded interactions in the conformational dynamics of organophosphorous hydrolase adsorbed onto functionalized mesoporous silica surfaces |
| Q56157182 | Time Integrators for Molecular Dynamics |
| Q39414163 | Topology mapping of insulin-regulated glucose transporter GLUT4 using computational biology. |
| Q90494763 | Toward Building Protein Force Fields by Residue-Based Systematic Molecular Fragmentation and Neural Network |
| Q96230372 | Toward Simple, Predictive Understanding of Protein-Ligand Interactions: Electronic Structure Calculations on Torpedo Californica Acetylcholinesterase Join Forces with the Chemist's Intuition |
| Q50457604 | Ultrafast molecular dynamics of biofuel extraction for microalgae and bacteria milking: blocking membrane folding pathways to damaged lipid-bilayer conformations with nanomicelles. |
| Q45917964 | Ultrafast structural dynamics of biomolecules examined by multiple-mode 2D IR spectroscopy: anharmonically coupled motions are in harmony. |
| Q47129907 | Uncovering Large-Scale Conformational Change in Molecular Dynamics without Prior Knowledge |
| Q91990826 | Understanding Missing Entropy in Coarse-Grained Systems: Addressing Issues of Representability and Transferability |
| Q41544769 | Understanding the binding of inhibitors of matrix metalloproteinases by molecular docking, quantum mechanical calculations, molecular dynamics simulations, and a MMGBSA/MMBappl study |
| Q33378588 | VSDMIP: virtual screening data management on an integrated platform. |
| Q62516585 | Validation of the GROMOS 54A7 Force Field Regarding Mixedα/β-Peptide Molecules |
| Q41955359 | Vibrational entropy differences between mesophile and thermophile proteins and their use in protein engineering |
| Q42740070 | Water dynamics in protein hydration shells: the molecular origins of the dynamical perturbation |
| Q54194507 | pH dependence of ligand-induced human epidermal growth factor receptor activation investigated by molecular dynamics simulations. |
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