Ensemble-Based Replica Exchange Alchemical Free Energy Methods: The Effect of Protein Mutations on Inhibitor Binding-Reference-Cited by-同舟云学术

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Ensemble-Based Replica Exchange Alchemical Free Energy Methods: The Effect of Protein Mutations on Inhibitor Binding

Published:2018-12-28 Issue:2 Volume:15 Page:1265-1277
ISSN:1549-9618
Container-title:Journal of Chemical Theory and Computation
language:en
Short-container-title:J. Chem. Theory Comput.

Author:

Bhati Agastya P.¹,Wan Shunzhou¹^ORCID,Coveney Peter V.¹^ORCID

Affiliation:

1. Centre for Computational Science, Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, United Kingdom

Funder

Medical Research Council

Qatar National Research Fund

H2020 Future and Emerging Technologies

H2020 Research Infrastructures

University College London

Division of Advanced Cyberinfrastructure

Inlaks Shivdasani Foundation

President & Provost?s Office, University College London

Publisher

American Chemical Society (ACS)

Subject

Physical and Theoretical Chemistry,Computer Science Applications

Link

http://pubs.acs.org/doi/pdf/10.1021/acs.jctc.8b01118

Reference33 articles.

1. From base pair to bedside: molecular simulation and the translation of genomics to personalized medicine

2. Accurate and Reliable Prediction of Relative Ligand Binding Potency in Prospective Drug Discovery by Way of a Modern Free-Energy Calculation Protocol and Force Field

3. Enhanced sampling techniques in molecular dynamics simulations of biological systems

4. Variational Approach to Enhanced Sampling and Free Energy Calculations

5. On the Hamiltonian replica exchange method for efficient sampling of biomolecular systems: Application to protein structure prediction

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2. Comparison of Equilibrium and Nonequilibrium Approaches for Relative Binding Free Energy Predictions;Journal of Chemical Theory and Computation;2023-10-20

3. Can Free Energy Perturbation Simulations Coupled with Replica-Exchange Molecular Dynamics Study Ligands with Distributed Binding Sites?;Journal of Chemical Information and Modeling;2023-08-02

4. Enhanced Configurational Sampling Approaches to Alchemical Ligand Binding Free Energy Simulations: Current Status and Challenges;The Journal of Physical Chemistry B;2023-07-27

5. Long Time Scale Ensemble Methods in Molecular Dynamics: Ligand–Protein Interactions and Allostery in SARS-CoV-2 Targets;Journal of Chemical Theory and Computation;2023-05-29

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