Standard binding free energies from computer simulations: What is the best strategy? (Q30540733)

17 August 2017

Standard binding free energies from computer simulations: What is the best strategy? (English)

1 reference

17 August 2017

0 references

1

James C Gumbart

1 reference

17 August 2017

Benoît Roux

2

1 reference

PMCID

3685508

17 August 2017

Christophe Chipot

series ordinal

3

1 reference

17 August 2017

1 January 2013

1 reference

Journal of Chemical Theory and Computation

17 August 2017

1 reference

17 August 2017

9

1 reference

17 August 2017

794-802

1 reference

17 August 2017

1

1 reference

Exploring Multidimensional Free Energy Landscapes Using Time-Dependent Biases on Collective Variables.

17 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3685508

All-atom empirical potential for molecular modeling and dynamics studies of proteins

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3685508

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3685508

Calculation of the Absolute Free Energy of Binding and Related Entropies with the HSMD-TI Method: The FKBP12-L8 Complex

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3685508

Absolute free energy of binding of avidin/biotin, revisited

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3685508

End-to-end attraction of duplex DNA.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3685508

Convergence and error estimation in free energy calculations using the weighted histogram analysis method

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3685508

Free Energy Perturbation Hamiltonian Replica-Exchange Molecular Dynamics (FEP/H-REMD) for Absolute Ligand Binding Free Energy Calculations

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3685508

Pathway and mechanism of drug binding to G-protein-coupled receptors.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3685508

Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3685508

Dual role of protein phosphorylation in DNA activator/coactivator binding

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3685508

New method for calculating the absolute free energy of binding: the effect of a mobile loop on the avidin/biotin complex

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3685508

Absolute binding free energy calculations: on the accuracy of computational scoring of protein-ligand interactions

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3685508

Predicting Ligand Binding Affinity with Alchemical Free Energy Methods in a Polar Model Binding Site

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3685508

Computations of standard binding free energies with molecular dynamics simulations

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3685508

Random walk in orthogonal space to achieve efficient free-energy simulation of complex systems

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3685508

Statistically optimal analysis of samples from multiple equilibrium states

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3685508

Binding specificity of SH2 domains: insight from free energy simulations

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3685508

Calculation of protein-ligand binding free energy by using a polarizable potential

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3685508

Predicting absolute ligand binding free energies to a simple model site

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3685508

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3685508

Computational analysis and prediction of the binding motif and protein interacting partners of the Abl SH3 domain

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3685508

Scalable molecular dynamics with NAMD

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3685508

Direct calculation of the binding free energies of FKBP ligands

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3685508

Calculation of absolute protein-ligand binding free energy from computer simulations

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3685508

Efficient evaluation of binding free energy using continuum electrostatics solvation

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3685508

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3685508

Energetics of ion conduction through the gramicidin channel

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3685508

Contribution of translational and rotational motions to molecular association in aqueous solution

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3685508

Crystal structure of the abl-SH3 domain complexed with a designed high-affinity peptide ligand: implications for SH3-ligand interactions

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3685508

The statistical-thermodynamic basis for computation of binding affinities: a critical review

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3685508

Molecular dynamics study of unbinding of the avidin-biotin complex

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3685508

Thermodynamic stability of water molecules in the bacteriorhodopsin proton channel: a molecular dynamics free energy perturbation study

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3685508

Rational design of specific high-affinity peptide ligands for the Abl-SH3 domain

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3685508

What determines the strength of noncovalent association of ligands to proteins in aqueous solution?

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3685508

Role of diffusion in ligand binding to macromolecules and cell-bound receptors

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3685508

Calculation of Standard Binding Free Energies: Aromatic Molecules in the T4 Lysozyme L99A Mutant.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3685508

Good practices in free-energy calculations

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3685508

Calculation of absolute protein-ligand binding free energy using distributed replica sampling

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3685508

Computing accurate potentials of mean force in electrolyte solutions with the generalized gradient-augmented harmonic Fourier beads method.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3685508

String method in collective variables: minimum free energy paths and isocommittor surfaces.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3685508

Simple estimation of absolute free energies for biomolecules.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3685508

Calculation of absolute protein-ligand binding affinity using path and endpoint approaches

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3685508

Overcoming free energy barriers using unconstrained molecular dynamics simulations

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3685508

Early mechanistic events in biotin dissociation from streptavidin

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3685508

Absolute free energy calculations by thermodynamic integration in four spatial dimensions

26 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23794960

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Standard Free Energy of Binding from a One-Dimensional Potential of Mean Force

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23794960

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1021/CT3008099

1 reference

17 August 2017

1 reference

17 August 2017

1 reference

PMCID

3685508