| scholarly article | Q13442814 |
| P50 | author | James C Gumbart | Q87700377 |
| P2093 | author name string | Benoît Roux | |
| Christophe Chipot | |||
| P2860 | cites work | What determines the strength of noncovalent association of ligands to proteins in aqueous solution? | Q24561579 |
| Predicting absolute ligand binding free energies to a simple model site | Q24683618 | ||
| Computational analysis and prediction of the binding motif and protein interacting partners of the Abl SH3 domain | Q25257719 | ||
| Predicting Ligand Binding Affinity with Alchemical Free Energy Methods in a Polar Model Binding Site | Q27657572 | ||
| Crystal structure of the abl-SH3 domain complexed with a designed high-affinity peptide ligand: implications for SH3-ligand interactions | Q27765076 | ||
| All-atom empirical potential for molecular modeling and dynamics studies of proteins | Q27860468 | ||
| Scalable molecular dynamics with NAMD | Q27860718 | ||
| Absolute free energy of binding of avidin/biotin, revisited | Q28385662 | ||
| Calculation of the Absolute Free Energy of Binding and Related Entropies with the HSMD-TI Method: The FKBP12-L8 Complex | Q28396455 | ||
| Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations | Q29547631 | ||
| Rational design of specific high-affinity peptide ligands for the Abl-SH3 domain | Q30176850 | ||
| Absolute binding free energy calculations: on the accuracy of computational scoring of protein-ligand interactions | Q30386091 | ||
| Statistically optimal analysis of samples from multiple equilibrium states | Q30438437 | ||
| Random walk in orthogonal space to achieve efficient free-energy simulation of complex systems | Q30485543 | ||
| Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations. | Q30501558 | ||
| Pathway and mechanism of drug binding to G-protein-coupled receptors. | Q30503489 | ||
| End-to-end attraction of duplex DNA. | Q30514058 | ||
| Efficient evaluation of binding free energy using continuum electrostatics solvation | Q33208396 | ||
| Calculation of absolute protein-ligand binding free energy from computer simulations | Q33784404 | ||
| Molecular dynamics study of unbinding of the avidin-biotin complex | Q33915230 | ||
| The statistical-thermodynamic basis for computation of binding affinities: a critical review | Q33915676 | ||
| Role of diffusion in ligand binding to macromolecules and cell-bound receptors | Q34255805 | ||
| Dual role of protein phosphorylation in DNA activator/coactivator binding | Q34494478 | ||
| Absolute binding free energy calculations using molecular dynamics simulations with restraining potentials | Q35051978 | ||
| Energetics of ion conduction through the gramicidin channel | Q35121583 | ||
| Free Energy Perturbation Hamiltonian Replica-Exchange Molecular Dynamics (FEP/H-REMD) for Absolute Ligand Binding Free Energy Calculations | Q35169555 | ||
| Convergence and error estimation in free energy calculations using the weighted histogram analysis method | Q35734759 | ||
| Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone φ, ψ and side-chain χ(1) and χ(2) dihedral angles | Q36546184 | ||
| Calculation of protein-ligand binding free energy by using a polarizable potential | Q36609140 | ||
| Binding specificity of SH2 domains: insight from free energy simulations | Q37083934 | ||
| Computations of standard binding free energies with molecular dynamics simulations | Q37335295 | ||
| Direct calculation of the binding free energies of FKBP ligands | Q39131231 | ||
| Contribution of translational and rotational motions to molecular association in aqueous solution | Q40190628 | ||
| New method for calculating the absolute free energy of binding: the effect of a mobile loop on the avidin/biotin complex | Q41912526 | ||
| Calculation of absolute protein-ligand binding affinity using path and endpoint approaches | Q42132116 | ||
| Thermodynamic stability of water molecules in the bacteriorhodopsin proton channel: a molecular dynamics free energy perturbation study | Q42536182 | ||
| Early mechanistic events in biotin dissociation from streptavidin | Q44074343 | ||
| Overcoming free energy barriers using unconstrained molecular dynamics simulations | Q45005453 | ||
| Computing accurate potentials of mean force in electrolyte solutions with the generalized gradient-augmented harmonic Fourier beads method. | Q45972773 | ||
| Calculation of absolute protein-ligand binding free energy using distributed replica sampling | Q46221592 | ||
| Good practices in free-energy calculations | Q46484190 | ||
| Exploring Multidimensional Free Energy Landscapes Using Time-Dependent Biases on Collective Variables. | Q51614241 | ||
| String method in collective variables: minimum free energy paths and isocommittor surfaces. | Q51937459 | ||
| Simple estimation of absolute free energies for biomolecules. | Q51945700 | ||
| Calculation of Standard Binding Free Energies: Aromatic Molecules in the T4 Lysozyme L99A Mutant. | Q53190267 | ||
| Absolute free energy calculations by thermodynamic integration in four spatial dimensions | Q81006447 | ||
| Standard Free Energy of Binding from a One-Dimensional Potential of Mean Force | Q86812273 | ||
| P433 | issue | 1 | |
| P921 | main subject | computer simulation | Q925667 |
| P304 | page(s) | 794-802 | |
| P577 | publication date | 2013-01-01 | |
| P1433 | published in | Journal of Chemical Theory and Computation | Q1768377 |
| P1476 | title | Standard binding free energies from computer simulations: What is the best strategy? | |
| P478 | volume | 9 |
| Q57787235 | A streamlined, general approach for computing ligand binding free energies and its application to GPCR-bound cholesterol |
| Q47567527 | Absolute binding free energies for octa-acids and guests in SAMPL5 : Evaluating binding free energies for octa-acid and guest complexes in the SAMPL5 blind challenge. |
| Q48043818 | Accurate Estimation of the Standard Binding Free Energy of Netropsin with DNA. |
| Q41993084 | Analyzing machupo virus-receptor binding by molecular dynamics simulations |
| Q51497789 | Anion-π interactions in complexes of proteins and halogen-containing amino acids. |
| Q90383206 | Application of the Movable Type Free Energy Method to the Caspase-Inhibitor BindingAffinity Study |
| Q55044864 | Aromatic Rings Commonly Used in Medicinal Chemistry: Force Fields Comparison and Interactions With Water Toward the Design of New Chemical Entities. |
| Q52345277 | Assessment of a Single Decoupling Alchemical Approach for the Calculation of the Absolute Binding Free Energies of Protein-Peptide Complexes. |
| Q38753477 | Attach-Pull-Release Calculations of Ligand Binding and Conformational Changes on the First BRD4 Bromodomain. |
| Q50060201 | BFEE: A User-Friendly Graphical Interface Facilitating Absolute Binding Free-Energy Calculations. |
| Q38291300 | Binding free energy calculations on E-selectin complexes with sLex oligosaccharide analogs |
| Q27679245 | Blind Prediction of Charged Ligand Binding Affinities in a Model Binding Site |
| Q30362300 | Bringing Clarity to the Prediction of Protein-Ligand Binding Free Energies via "Blurring" |
| Q45710657 | Calculating binding free energies of host-guest systems using the AMOEBA polarizable force field |
| Q50791393 | Calculating the free energy of transfer of small solutes into a model lipid membrane: Comparison between metadynamics and umbrella sampling. |
| Q33919788 | Chemomechanical Coupling in Hexameric Protein-Protein Interfaces Harnesses Energy within V-Type ATPases |
| Q89083748 | Comparing alchemical and physical pathway methods for computing the absolute binding free energy of charged ligands |
| Q38935370 | Computational Approaches to the Chemical Equilibrium Constant in Protein-ligand Binding |
| Q92923684 | Computational Modeling of Claudin Structure and Function |
| Q36552694 | Computational Studies of Molecular Permeation through Connexin26 Channels |
| Q40543300 | Computing Protein-Protein Association Affinity with Hybrid Steered Molecular Dynamics |
| Q51227911 | Computing the binding affinity of a ligand buried deep inside a protein with the hybrid steered molecular dynamics. |
| Q35661490 | Cooperative DNA Recognition Modulated by an Interplay between Protein-Protein Interactions and DNA-Mediated Allostery |
| Q27704012 | Crystal structure of the deglycating enzyme Amadoriase I in its free form and substrate-bound complex |
| Q39328873 | D3R grand challenge 2015: Evaluation of protein-ligand pose and affinity predictions |
| Q38742285 | Dissociation of a Dynamic Protein Complex Studied by All-Atom Molecular Simulations |
| Q37257220 | Efficient determination of protein-protein standard binding free energies from first principles |
| Q38291434 | Estimating glycosaminoglycan-protein interaction affinity: water dominates the specific antithrombin-heparin interaction |
| Q37212883 | Free Energy Landscape of Lipid Interactions with Regulatory Binding Sites on the Transmembrane Domain of the EGF Receptor |
| Q30539051 | Funnel metadynamics as accurate binding free-energy method |
| Q33763745 | Generalized Scalable Multiple Copy Algorithms for Molecular Dynamics Simulations in NAMD. |
| Q39989280 | Hybrid Steered Molecular Dynamics Approach to Computing Absolute Binding Free Energy of Ligand-Protein Complexes: A Brute Force Approach That Is Fast and Accurate |
| Q50643424 | I. Dissociation free energies of drug-receptor systems via non-equilibrium alchemical simulations: a theoretical framework. |
| Q46546512 | II. Dissociation free energies in drug-receptor systems via nonequilibrium alchemical simulations: application to the FK506-related immunophilin ligands. |
| Q35871478 | Influence of Chirality of Crizotinib on Its MTH1 Protein Inhibitory Activity: Insight from Molecular Dynamics Simulations and Binding Free Energy Calculations |
| Q98568595 | Ligand binding free-energy calculations with funnel metadynamics |
| Q57275094 | Ligand induced change of β2adrenergic receptor from active to inactive conformation and its implication for the closed/open state of the water channel: insight from molecular dynamics simulation, free energy calculation and Markov state model analys |
| Q42142586 | Mechanism of mRNA-STAR domain interaction: Molecular dynamics simulations of Mammalian Quaking STAR protein |
| Q35021715 | Mechanistic insights into a classic wonder drug--aspirin |
| Q47229442 | Method evaluations for adsorption free energy calculations at solid/water interface via metadynamics, umbrella sampling and Jarzynski's equality. |
| Q33919887 | Methodology for the Simulation of Molecular Motors at Different Scales |
| Q45943917 | Modern drug design: the implication of using artificial neuronal networks and multiple molecular dynamic simulations. |
| Q37184211 | Molecular Mechanism of Processive 3' to 5' RNA Translocation in the Active Subunit of the RNA Exosome Complex |
| Q39164064 | Molecular Simulations of Disulfide-Rich Venom Peptides with Ion Channels and Membranes |
| Q59892649 | Molecular Simulations of Thermodynamic Properties for the System α -Cyclodextrin/Alcohol in Aqueous Solution |
| Q93159431 | Molecular dynamics simulations of nucleotide release from the circadian clock protein KaiC reveal atomic-resolution functional insights |
| Q42577895 | Molecular dynamics simulations on the effect of size and shape on the interactions between negative Au18(SR)14, Au102(SR)44 and Au144(SR)60 nanoparticles in physiological saline. |
| Q39181234 | Multiple binding modes of ibuprofen in human serum albumin identified by absolute binding free energy calculations |
| Q43013072 | Net charge changes in the calculation of relative ligand-binding free energies via classical atomistic molecular dynamics simulation |
| Q52353173 | New tricks for old dogs: improving the accuracy of biomolecular force fields by pair-specific corrections to non-bonded interactions. |
| Q41972661 | Overcoming dissipation in the calculation of standard binding free energies by ligand extraction |
| Q38818618 | Overview of the SAMPL5 host-guest challenge: Are we doing better? |
| Q28540825 | P-loop conformation governed crizotinib resistance in G2032R-mutated ROS1 tyrosine kinase: clues from free energy landscape |
| Q39235195 | Predicting Binding Free Energies: Frontiers and Benchmarks |
| Q54124846 | Predicting the Conformational Variability of Abl Tyrosine Kinase using Molecular Dynamics Simulations and Markov State Models. |
| Q48053583 | Proton-Coupled Conformational Allostery Modulates the Inhibitor Selectivity for β-Secretase |
| Q47302876 | Quantitative Assessment of the Energetics of Dopamine Translocation by Human Dopamine Transporter |
| Q46096236 | Resolving the Ligand-Binding Specificity in c-MYC G-Quadruplex DNA: Absolute Binding Free Energy Calculations and SPR Experiment |
| Q35080674 | Revealing the favorable dissociation pathway of type II kinase inhibitors via enhanced sampling simulations and two-end-state calculations |
| Q53646355 | Selectivity of pyoverdine recognition by the FpvA receptor of Pseudomonas aeruginosa from molecular dynamics simulations. |
| Q41674692 | Statistical Analysis on the Performance of Molecular Mechanics Poisson-Boltzmann Surface Area versus Absolute Binding Free Energy Calculations: Bromodomains as a Case Study |
| Q36939233 | Study on the Application of the Combination of TMD Simulation and Umbrella Sampling in PMF Calculation for Molecular Conformational Transitions |
| Q92147348 | Systematic Mutagenesis of Oncocin Reveals Enhanced Activity and Insights into the Mechanisms of Antimicrobial Activity |
| Q47303291 | Systematic Testing of Belief-Propagation Estimates for Absolute Free Energies in Atomistic Peptides and Proteins |
| Q47160051 | The Molecular Tweezer CLR01 Stabilizes a Disordered Protein-Protein Interface. |
| Q35012592 | The adaptive biasing force method: everything you always wanted to know but were afraid to ask |
| Q33727589 | The cis conformation of proline leads to weaker binding of a p53 peptide to MDM2 compared to trans. |
| Q47828652 | The role of solvation in the binding selectivity of the L-type calcium channel. |
| Q96432433 | Thermodynamic Integration in 3n Dimensions without Biases or Alchemy for Protein Interactions |
| Q50214049 | Thermodynamics of DNA: sensitizer recognition. Characterizing binding motifs with all-atom simulations. |
| Q51725885 | Thermodynamics of complex structures formed between single-stranded DNA oligomers and the KH domains of the far upstream element binding protein. |
| Q38928891 | Toward the identification of molecular cogs |
| Q28546110 | Uncovering Molecular Bases Underlying Bone Morphogenetic Protein Receptor Inhibitor Selectivity |
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