(Q35169555)

6 August 2017

title

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

1 reference

6 August 2017

1 reference

Wei Jiang

1

1 reference

6 August 2017

Benoît Roux

series ordinal

2

1 reference

6 August 2017

publication date

1 July 2010

1 reference

Journal of Chemical Theory and Computation

6 August 2017

published in

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6 August 2017

volume

6

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6 August 2017

issue

9

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6 August 2017

page(s)

2559-2565

1 reference

A Hamiltonian Replica Exchange Approach and Its Application to the Study of Side-Chain Type and Neighbor Effects on Peptide Backbone Conformations

6 August 2017

cites work

1 reference

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

28 July 2018

1 reference

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Computation of Absolute Hydration and Binding Free Energy with Free Energy Perturbation Distributed Replica-Exchange Molecular Dynamics (FEP/REMD).

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3157700

Replica-Exchange Accelerated Molecular Dynamics (REXAMD) Applied to Thermodynamic Integration

28 July 2018

1 reference

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CHARMM: the biomolecular simulation program

28 July 2018

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The Confine-and-Release Method: Obtaining Correct Binding Free Energies in the Presence of Protein Conformational Change

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3157700

Binding specificity of SH2 domains: insight from free energy simulations

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3157700

Predicting absolute ligand binding free energies to a simple model site

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3157700

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3157700

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3157700

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

28 July 2018

1 reference

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Efficient free energy calculations for compounds with multiple stable conformations separated by high energy barriers

27 September 2018

1 reference

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Efficient drug lead discovery and optimization

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3157700

Hamiltonian replica exchange molecular dynamics using soft-core interactions

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3157700

Enhanced sampling of peptide and protein conformations using replica exchange simulations with a peptide backbone biasing-potential.

27 September 2018

1 reference

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Accelerated molecular dynamics: a promising and efficient simulation method for biomolecules

27 September 2018

1 reference

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Specificity of ligand binding in a buried nonpolar cavity of T4 lysozyme: linkage of dynamics and structural plasticity

27 September 2018

1 reference

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Interfacing Q-Chem and CHARMM to perform QM/MM reaction path calculations

27 September 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21857813

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1021/CT1001768

1 reference

6 August 2017

1 reference

6 August 2017

1 reference