Uncertainty Quantification in Alchemical Free Energy Methods

scientific article published on 02 May 2018

Uncertainty Quantification in Alchemical Free Energy Methods is …
instance of (P31):
scholarly articleQ13442814

External links are
P356DOI10.1021/ACS.JCTC.7B01143
P932PMC publication ID6095638
P698PubMed publication ID29678106

P50authorPeter CoveneyQ7173422
Shunzhou WanQ61826316
Yuan HuQ57033149
Agastya P BhatiQ61826313
P2093author name stringBrad Sherborne
P2860cites workWhy most published research findings are falseQ21092395
Predicting absolute ligand binding free energies to a simple model siteQ24683618
Gaussian Accelerated Molecular Dynamics: Unconstrained Enhanced Sampling and Free Energy CalculationQ27301372
Predicting Ligand Binding Affinity with Alchemical Free Energy Methods in a Polar Model Binding SiteQ27657572
Scalable molecular dynamics with NAMDQ27860718
The Amber biomolecular simulation programsQ27860745
Big data need big theory tooQ28077643
Predictions of Ligand Selectivity from Absolute Binding Free Energy CalculationsQ28818600
Development and testing of a general amber force fieldQ29547642
Statistically optimal analysis of samples from multiple equilibrium statesQ30438437
Molecular recognition in a diverse set of protein-ligand interactions studied with molecular dynamics simulations and end-point free energy calculationsQ33758074
Steered molecular dynamics and mechanical functions of proteinsQ33942097
Replica exchange with solute tempering: a method for sampling biological systems in explicit waterQ34048139
Escaping free-energy minimaQ34151010
Accurate and reliable prediction of relative ligand binding potency in prospective drug discovery by way of a modern free-energy calculation protocol and force fieldQ34459931
Absolute binding free energy calculations using molecular dynamics simulations with restraining potentialsQ35051978
Rapid and accurate ranking of binding affinities of epidermal growth factor receptor sequences with selected lung cancer drugsQ35059352
Enhanced sampling techniques in molecular dynamics simulations of biological systemsQ35118094
Replica exchange with solute scaling: a more efficient version of replica exchange with solute tempering (REST2).Q35212444
Free energy calculations by computer simulationQ69004087
A comparison of different initialization protocols to obtain statistically independent molecular dynamics simulationsQ82744331
Accurate predictions of nonpolar solvation free energies require explicit consideration of binding-site hydrationQ84505378
ORAC: a molecular dynamics simulation program to explore free energy surfaces in biomolecular systems at the atomistic levelQ84708455
Computational Analysis of the Mechanism and Thermodynamics of Inhibition of Phosphodiesterase 5A by Synthetic LigandsQ86840750
On the calculation of equilibrium thermodynamic properties from molecular dynamicsQ89407775
On achieving high accuracy and reliability in the calculation of relative protein-ligand binding affinitiesQ35751099
The Effect of Mutations on Drug Sensitivity and Kinase Activity of Fibroblast Growth Factor Receptors: A Combined Experimental and Theoretical StudyQ35752926
Progress in the development of synthetic thrombin inhibitors as new orally active anticoagulantsQ35893038
Theory of binless multi-state free energy estimation with applications to protein-ligand bindingQ35921319
Locally accessible conformations of proteins: multiple molecular dynamics simulations of crambinQ36280885
Accurate calculation of the absolute free energy of binding for drug moleculesQ36427764
How consistent are molecular dynamics simulations? Comparing structure and dynamics in reduced and oxidized Escherichia coli thioredoxin.Q36774122
Independent-Trajectories Thermodynamic-Integration Free-Energy Changes for Biomolecular Systems: Determinants of H5N1 Avian Influenza Virus Neuraminidase Inhibition by PeramivirQ37159181
Using multistate free energy techniques to improve the efficiency of replica exchange accelerated molecular dynamicsQ37237147
Calculating the binding free energies of charged species based on explicit-solvent simulations employing lattice-sum methods: an accurate correction scheme for electrostatic finite-size effectsQ37337108
Parallel tempering: theory, applications, and new perspectivesQ37610077
Rapid and Reliable Binding Affinity Prediction of Bromodomain Inhibitors: A Computational Study.Q37646303
Computing Clinically Relevant Binding Free Energies of HIV-1 Protease Inhibitors.Q37665027
Advanced replica-exchange sampling to study the flexibility and plasticity of peptides and proteinsQ38072502
A long journey to reproducible resultsQ38556862
Free energy via molecular simulation: applications to chemical and biomolecular systemsQ38648060
Validation of Molecular Simulation: An Overview of IssuesQ38691259
Evaluation and Characterization of Trk Kinase Inhibitors for the Treatment of Pain: Reliable Binding Affinity Predictions from Theory and ComputationQ38893670
Rapid, Accurate, Precise, and Reliable Relative Free Energy Prediction Using Ensemble Based Thermodynamic IntegrationQ39084152
Starting structure dependence of NMR order parameters derived from MD simulations: implications for judging force-field qualityQ39123482
Direct calculation of the binding free energies of FKBP ligandsQ39131231
Rapid, Precise, and Reproducible Prediction of Peptide-MHC Binding Affinities from Molecular Dynamics That Correlate Well with ExperimentQ40314015
Structure-based drug design: computational advances.Q41455713
Accurate ensemble molecular dynamics binding free energy ranking of multidrug-resistant HIV-1 proteasesQ43103118
Constant pH molecular dynamics in generalized Born implicit solventQ43734394
Calculation of protein ionization equilibria with conformational sampling: pK(a) of a model leucine zipper, GCN4 and barnaseQ43825576
1,500 scientists lift the lid on reproducibilityQ44039870
Enhanced sampling by multiple molecular dynamics trajectories: carbonmonoxy myoglobin 10 micros A0-->A(1-3) transition from ten 400 picosecond simulationsQ44853010
How to obtain statistically converged MM/GBSA results.Q45929672
Adaptive biasing force method for scalar and vector free energy calculationsQ46830946
Binding affinities of the farnesoid X receptor in the D3R Grand Challenge 2 estimated by free-energy perturbation and docking.Q48023567
Toward Fast and Accurate Binding Affinity Prediction with pmemdGTI: An Efficient Implementation of GPU-Accelerated Thermodynamic IntegrationQ48271066
Graphene-Graphene Interactions: Friction, Superlubricity, and Exfoliation.Q50050054
The Effect of Conformational Flexibility on Binding Free Energy Estimation between Kinases and Their Inhibitors.Q51235291
Binding affinities of factor Xa inhibitors estimated by thermodynamic integration and MM/GBSA.Q51590039
Assessing the stability of free-energy perturbation calculations by performing variations in the method.Q55037679
Reproducibility: Check your chemistryQ59068868
P433issue6
P304page(s)2867-2880
P577publication date2018-05-02
P1433published inJournal of Chemical Theory and ComputationQ1768377
P1476titleUncertainty Quantification in Alchemical Free Energy Methods
P478volume14

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cites work (P2860)
Q64052941Application of ESMACS binding free energy protocols to diverse datasets: Bromodomain-containing protein 4
Q92581710Effect of mutations on binding of ligands to guanine riboswitch probed by free energy perturbation and molecular dynamics simulations
Q90348968Fast, Accurate, and Reliable Protocols for Routine Calculations of Protein-Ligand Binding Affinities in Drug Design Projects Using AMBER GPU-TI with ff14SB/GAFF
Q60937560High-throughput binding affinity calculations at extreme scales

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