Absolute binding free energy calculations using molecular dynamics simulations with restraining potentials

scientific article

Absolute binding free energy calculations using molecular dynamics simulations with restraining potentials is …
instance of (P31):
scholarly articleQ13442814

External links are
P356DOI10.1529/BIOPHYSJ.106.084301
P932PMC publication ID1578458
P698PubMed publication ID16844742
P5875ResearchGate publication ID6940573

P2093author name stringBenoît Roux
Jiyao Wang
Yuqing Deng
P2860cites work"New view" of protein folding reconciled with the old through multiple unfolding simulations.Q52528318
Free Energy Landscape of A-DNA to B-DNA Conversion in Aqueous SolutionQ56770488
An Efficient Mean Solvation Force Model for Use in Molecular Dynamics Simulations of Proteins in Aqueous SolutionQ57950560
Optimized Monte Carlo data analysisQ59732808
Computational binding studies of human pp60c-src SH2 domain with a series of nonpeptide, phosphophenyl-containing ligandsQ74351332
Estimation of the binding affinities of FKBP12 inhibitors using a linear response methodQ77984420
Crystal structures of human calcineurin and the human FKBP12-FK506-calcineurin complexQ24310797
Atomic solvation parameters applied to molecular dynamics of proteins in solutionQ24676145
X-ray structure of calcineurin inhibited by the immunophilin-immunosuppressant FKBP12-FK506 complexQ27729433
Implicit solvent modelsQ28267646
Atomic structure of FKBP-FK506, an immunophilin-immunosuppressant complexQ28273179
Solvation energy in protein folding and bindingQ28307568
Development and testing of a general amber force fieldQ29547642
Classical electrostatics in biology and chemistryQ29615082
Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum modelsQ29616389
Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validationQ29617869
The N-terminal end of the catalytic domain of SRC kinase Hck is a conformational switch implicated in long-range allosteric regulationQ30160076
Developing a dynamic pharmacophore model for HIV-1 integrase.Q30326870
Virtual screening and fast automated docking methods.Q30329412
On the nonpolar hydration free energy of proteins: surface area and continuum solvent models for the solute-solvent interaction energy.Q30333244
Design of RNA-binding proteins and ligandsQ30699653
Molecular dynamics simulations of biomolecules: long-range electrostatic effectsQ33689931
Energetic dissection of specificity in serine proteasesQ33696239
Calculation of absolute protein-ligand binding free energy from computer simulationsQ33784404
The statistical-thermodynamic basis for computation of binding affinities: a critical reviewQ33915676
On the calculation of absolute macromolecular binding free energiesQ34074487
Revisiting free energy calculations: a theoretical connection to MM/PBSA and direct calculation of the association free energyQ34184435
Computational methods to predict binding free energy in ligand-receptor complexesQ34369739
Recognition of specific DNA sequences.Q34462035
Free energy simulations come of age: protein-ligand recognitionQ34691182
Chemistry and Biology of the Immunophilins and Their Immunosuppressive LigandsQ36617985
Free energy via molecular simulation: applications to chemical and biomolecular systemsQ38648060
Direct calculation of the binding free energies of FKBP ligandsQ39131231
Excluded volume approximation to protein-solvent interaction. The solvent contact modelQ39628335
Atomic solvation parameters in the analysis of protein-protein docking resultsQ42076740
Calculation of absolute protein-ligand binding affinity using path and endpoint approachesQ42132116
Thermodynamic stability of water molecules in the bacteriorhodopsin proton channel: a molecular dynamics free energy perturbation studyQ42536182
Estimation of binding affinities for celecoxib analogues with COX-2 via Monte Carlo-extended linear responseQ43868923
Contributions to the binding free energy of ligands to avidin and streptavidin.Q43947466
Theory of biomolecular recognitionQ46853640
Comparative X-ray structures of the major binding protein for the immunosuppressant FK506 (tacrolimus) in unliganded form and in complex with FK506 and rapamycinQ47982867
Grand canonical Monte Carlo simulations of water in protein environments.Q51988450
Evaluation of protein-protein association energies by free energy perturbation calculations.Q52078727
Ligand solvation in molecular docking.Q52214239
P4510describes a project that usesmolecular dynamics simulationQ901663
P433issue8
P407language of work or nameEnglishQ1860
P304page(s)2798-2814
P577publication date2006-07-14
P1433published inBiophysical JournalQ2032955
P1476titleAbsolute binding free energy calculations using molecular dynamics simulations with restraining potentials
P478volume91

Reverse relations

cites work (P2860)
Q28304560A machine learning-based method to improve docking scoring functions and its application to drug repurposing
Q36601750A simplified confinement method for calculating absolute free energies and free energy and entropy differences
Q57787235A streamlined, general approach for computing ligand binding free energies and its application to GPCR-bound cholesterol
Q42729386Absolute FKBP binding affinities obtained via nonequilibrium unbinding simulations
Q39343604Accounting for ligand conformational restriction in calculations of protein-ligand binding affinities
Q37063817Accurate calculation of mutational effects on the thermodynamics of inhibitor binding to p38α MAP kinase: a combined computational and experimental study
Q36427764Accurate calculation of the absolute free energy of binding for drug molecules
Q34083570Accurate prediction of the binding free energy and analysis of the mechanism of the interaction of replication protein A (RPA) with ssDNA.
Q34590635Activation of the edema factor of Bacillus anthracis by calmodulin: evidence of an interplay between the EF-calmodulin interaction and calcium binding
Q90381064Adapting free energy perturbation simulations for large macrocyclic ligands: how to dissect contributions from direct binding and free ligand flexibility
Q30427576Alchemical free energy methods for drug discovery: progress and challenges
Q50938773Ammonium scanning in an enzyme active site. The chiral specificity of aspartyl-tRNA synthetase.
Q28482424An efficient computational method for calculating ligand binding affinities
Q33712042An improved strategy for generating forces in steered molecular dynamics: the mechanical unfolding of titin, e2lip3 and ubiquitin
Q101038765An in-silico layer-by-layer adsorption study of the interaction between Rebaudioside A and the T1R2 human sweet taste receptor: modelling and biosensing perspectives
Q41993084Analyzing machupo virus-receptor binding by molecular dynamics simulations
Q36802557Application of a polarizable force field to calculations of relative protein-ligand binding affinities
Q39597289Application of binding free energy calculations to prediction of binding modes and affinities of MDM2 and MDMX inhibitors
Q50060201BFEE: A User-Friendly Graphical Interface Facilitating Absolute Binding Free-Energy Calculations.
Q30392142Beyond Membrane Protein Structure: Drug Discovery, Dynamics and Difficulties
Q92315774Binding Modes and Metabolism of Caffeine
Q55476262Binding Modes of Ligands Using Enhanced Sampling (BLUES): Rapid Decorrelation of Ligand Binding Modes via Nonequilibrium Candidate Monte Carlo.
Q37372747Binding of small-molecule ligands to proteins: "what you see" is not always "what you get".
Q38344912Binding selectivity of RecA to a single stranded DNA, a computational approach
Q37083934Binding specificity of SH2 domains: insight from free energy simulations
Q27679245Blind Prediction of Charged Ligand Binding Affinities in a Model Binding Site
Q30362300Bringing Clarity to the Prediction of Protein-Ligand Binding Free Energies via "Blurring"
Q38793733CHARMM-GUI 10 years for biomolecular modeling and simulation
Q36569443CHARMM-GUI Ligand Binder for absolute binding free energy calculations and its application
Q24658108CHARMM: the biomolecular simulation program
Q37337108Calculating the binding free energies of charged species based on explicit-solvent simulations employing lattice-sum methods: an accurate correction scheme for electrostatic finite-size effects
Q36609140Calculation of protein-ligand binding free energy by using a polarizable potential
Q28396455Calculation of the Absolute Free Energy of Binding and Related Entropies with the HSMD-TI Method: The FKBP12-L8 Complex
Q45934140Can Relative Binding Free Energy Predict Selectivity of Reversible Covalent Inhibitors?
Q38297777Cello-oligomer-binding dynamics and directionality in family 4 carbohydrate-binding modules.
Q89893213Combining Alchemical Transformation with a Physical Pathway to Accelerate Absolute Binding Free Energy Calculations of Charged Ligands to Enclosed Binding Sites
Q34290068Comprehensive interrogation of natural TALE DNA-binding modules and transcriptional repressor domains
Q35169470Computation of Absolute Hydration and Binding Free Energy with Free Energy Perturbation Distributed Replica-Exchange Molecular Dynamics (FEP/REMD).
Q44694277Computation of binding free energy with molecular dynamics and grand canonical Monte Carlo simulations
Q39551290Computation of relative binding free energy for an inhibitor and its analogs binding with Erk kinase using thermodynamic integration MD simulation.
Q51604061Computation of the binding affinities of catechol-O-methyltransferase inhibitors: multisubstate relative free energy calculations.
Q38935370Computational Approaches to the Chemical Equilibrium Constant in Protein-ligand Binding
Q33631185Computational analysis of the binding specificity of Gleevec to Abl, c-Kit, Lck, and c-Src tyrosine kinases
Q37375373Computational evaluation of protein-small molecule binding.
Q28475699Computational fragment-based binding site identification by ligand competitive saturation
Q35728158Computational investigation of glycosylation effects on a family 1 carbohydrate-binding module
Q45984542Computational studies of human galectin-1: role of conserved tryptophan residue in stacking interaction with carbohydrate ligands.
Q34408156Computational study of Gleevec and G6G reveals molecular determinants of kinase inhibitor selectivity
Q37335295Computations of standard binding free energies with molecular dynamics simulations
Q92613345Computing Relative Binding Affinity of Ligands to Receptor: An Effective Hybrid Single-Dual-Topology Free-Energy Perturbation Approach in NAMD
Q35773629Conformational Transitions and Convergence of Absolute Binding Free Energy Calculations
Q33533343Conformational dynamics and ligand binding in the multi-domain protein PDC109
Q28066484Constraint methods that accelerate free-energy simulations of biomolecules
Q30457582Converging free energies of binding in cucurbit[7]uril and octa-acid host-guest systems from SAMPL4 using expanded ensemble simulations
Q35661490Cooperative DNA Recognition Modulated by an Interplay between Protein-Protein Interactions and DNA-Mediated Allostery
Q27704012Crystal structure of the deglycating enzyme Amadoriase I in its free form and substrate-bound complex
Q35136572Current progress in Structure-Based Rational Drug Design marks a new mindset in drug discovery
Q41989179Distinguishing binders from false positives by free energy calculations: fragment screening against the flap site of HIV protease
Q34494478Dual role of protein phosphorylation in DNA activator/coactivator binding
Q92931151Effect of Dimethyl Sulfoxide on the Binding of 1-Adamantane Carboxylic Acid to β- and γ-Cyclodextrins
Q37624587Effects of hypoxanthine substitution in peptide nucleic acids targeting KRAS2 oncogenic mRNA molecules: theory and experiment
Q42780060Elucidating the energetics of entropically driven protein-ligand association: calculations of absolute binding free energy and entropy
Q42371317Energetics of double-ion occupancy in the gramicidin A channel
Q59349138Enhanced Monte Carlo Methods for Modeling Proteins Including Computation of Absolute Free Energies of Binding
Q39257749Evaluation of protein-ligand affinity prediction using steered molecular dynamics simulations
Q36582978Explaining why Gleevec is a specific and potent inhibitor of Abl kinase
Q28386158Extending fragment-based free energy calculations with library Monte Carlo simulation: annealing in interaction space
Q36604456Force Field for Mg(2+), Mn(2+), Zn(2+), and Cd(2+) Ions That Have Balanced Interactions with Nucleic Acids
Q35169555Free Energy Perturbation Hamiltonian Replica-Exchange Molecular Dynamics (FEP/H-REMD) for Absolute Ligand Binding Free Energy Calculations
Q39645443Free energy calculations on snake venom metalloproteinase BaP1.
Q90683085Free-energy landscape of molecular interactions between endothelin 1 and human endothelin type B receptor: fly-casting mechanism
Q30414700Free-energy simulations reveal that both hydrophobic and polar interactions are important for influenza hemagglutinin antibody binding
Q33763745Generalized Scalable Multiple Copy Algorithms for Molecular Dynamics Simulations in NAMD.
Q37202836Hunting for predictive computational drug-discovery models
Q41998223Hybrid Steered Molecular Dynamics-Docking: An Efficient Solution to the Problem of Ranking Inhibitor Affinities Against a Flexible Drug Target
Q50643424I. Dissociation free energies of drug-receptor systems via non-equilibrium alchemical simulations: a theoretical framework.
Q46546512II. Dissociation free energies in drug-receptor systems via nonequilibrium alchemical simulations: application to the FK506-related immunophilin ligands.
Q47406205Impact of domain knowledge on blinded predictions of binding energies by alchemical free energy calculations
Q44076075In silico profiling and structural insights of missense mutations in RET protein kinase domain by molecular dynamics and docking approach
Q37209057Inhibition versus potentiation of ligand-gated ion channels can be altered by a single mutation that moves ligands between intra- and intersubunit sites
Q38684570Insights into Ligand-Protein Binding from Local Mechanical Response.
Q47788364Interactions of calmodulin with death-associated protein kinase peptides: experimental and modeling studies
Q85857386Investigating Molecular Mechanisms of Activation and Mutation of the HER2 Receptor Tyrosine Kinase through Computational Modeling and Simulation
Q37464148Ligand and structure-based methodologies for the prediction of the activity of G protein-coupled receptor ligands
Q42633034Ligand binding to the voltage-gated Kv1.5 potassium channel in the open state--docking and computer simulations of a homology model
Q40420002Limits of Free Energy Computation for Protein-Ligand Interactions
Q47948501Massively parallel computation of absolute binding free energy with well-equilibrated states
Q33427227Mechanism and energetics of charybdotoxin unbinding from a potassium channel from molecular dynamics simulations
Q45846360Mechanistic insights into Pin1 peptidyl-prolyl cis-trans isomerization from umbrella sampling simulations
Q46221653Modeling molecular and ionic absolute solvation free energies with quasichemical theory bounds
Q45943917Modern drug design: the implication of using artificial neuronal networks and multiple molecular dynamic simulations.
Q28551549Molecular Dynamics Assisted Mechanistic Study of Isoniazid-Resistance against Mycobacterium tuberculosis InhA
Q34061019Molecular dynamics simulations and drug discovery
Q93159431Molecular dynamics simulations of nucleotide release from the circadian clock protein KaiC reveal atomic-resolution functional insights
Q34932216Molecular dynamics study of zinc binding to cysteines in a peptide mimic of the alcohol dehydrogenase structural zinc site.
Q36957325Molecular mechanism of ion-ion and ion-substrate coupling in the Na+-dependent leucine transporter LeuT.
Q30157892On the importance of a funneled energy landscape for the assembly and regulation of multidomain Src tyrosine kinases
Q47392894On the selectivity of the NaChBac channel: an integrated computational and experimental analysis of sodium and calcium permeation
Q36678118Pathway and endpoint free energy calculations for cyclic nucleotide binding to HCN channels
Q42032808Polymorphism of the epidermal growth factor receptor extracellular ligand binding domain: the dimer interface depends on domain stabilization
Q55384303Precision therapeutic targeting of human cancer cell motility.
Q27657572Predicting Ligand Binding Affinity with Alchemical Free Energy Methods in a Polar Model Binding Site
Q24683618Predicting absolute ligand binding free energies to a simple model site
Q37761334Prediction of protein-ligand binding affinity by free energy simulations: assumptions, pitfalls and expectations
Q30432314Probing carbohydrate product expulsion from a processive cellulase with multiple absolute binding free energy methods
Q45923228Probing hot spots on protein-protein interfaces with all-atom free-energy simulation.
Q38302459Probing substrate interactions in the active tunnel of a catalytically deficient cellobiohydrolase (Cel7)
Q38124417Protonation and pK changes in protein-ligand binding.
Q36243073Recent theoretical and computational advances for modeling protein-ligand binding affinities
Q57038883Reduced Free Energy Perturbation/Hamiltonian Replica Exchange Molecular Dynamics Method with Unbiased Alchemical Thermodynamic Axis
Q37118439Replica-Exchange Accelerated Molecular Dynamics (REXAMD) Applied to Thermodynamic Integration
Q36688022Separated topologies--a method for relative binding free energy calculations using orientational restraints
Q35566613Site Identification by Ligand Competitive Saturation (SILCS) simulations for fragment-based drug design
Q30540733Standard binding free energies from computer simulations: What is the best strategy?
Q35794917Statistical mechanics and molecular dynamics in evaluating thermodynamic properties of biomolecular recognition
Q37191990Structural and functional basis of a role for CRKL in a fibroblast growth factor 8-induced feed-forward loop
Q37750881Structural ensemble in computational drug screening
Q34690517Structure-affinity properties of a high-affinity ligand of FKBP12 studied by molecular simulations of a binding intermediate
Q36939233Study on the Application of the Combination of TMD Simulation and Umbrella Sampling in PMF Calculation for Molecular Conformational Transitions
Q34352706The Binding Energy Distribution Analysis Method (BEDAM) for the Estimation of Protein-Ligand Binding Affinities
Q30372513The Confine-and-Release Method: Obtaining Correct Binding Free Energies in the Presence of Protein Conformational Change
Q33727589The cis conformation of proline leads to weaker binding of a p53 peptide to MDM2 compared to trans.
Q34611548The mechanism of H171T resistance reveals the importance of Nδ-protonated His171 for the binding of allosteric inhibitor BI-D to HIV-1 integrase
Q42909481The mechanism of a neurotransmitter:sodium symporter--inward release of Na+ and substrate is triggered by substrate in a second binding site
Q35342488The structural pathway for water permeation through sodium-glucose cotransporters
Q35921319Theory of binless multi-state free energy estimation with applications to protein-ligand binding
Q28383645Theory of free energy and entropy in noncovalent binding
Q51030409Thermodynamics of surface defects at the aspirin/water interface.
Q57275096Toward energy efficiency in heterogeneous processors: findings on virtual screening methods
Q44207658Transferable scoring function based on semiempirical quantum mechanical PM6-DH2 method: CDK2 with 15 structurally diverse inhibitors.
Q88424164Uncertainty Quantification in Alchemical Free Energy Methods
Q33940014Using free energy of binding calculations to improve the accuracy of virtual screening predictions
Q33815031Virtual high-throughput ligand screening

Search more.