Calculation of adsorption free energy for solute-surface interactions using biased replica-exchange molecular dynamics

Feng Wang; Steven J. Stuart; Robert A. Latour

doi:10.1116/1.2840054

Calculation of adsorption free energy for solute-surface interactions using biased replica-exchange molecular dynamics

Biointerphases ◽

10.1116/1.2840054 ◽

2008 ◽

Vol 3 (1) ◽

pp. 9-18 ◽

Cited By ~ 38

Author(s):

Feng Wang ◽

Steven J. Stuart ◽

Robert A. Latour

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Surface Interactions ◽

Replica Exchange ◽

Replica Exchange Molecular Dynamics ◽

Adsorption Free Energy

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Free Energy Surface of an Intrinsically Disordered Protein: Comparison between Temperature Replica Exchange Molecular Dynamics and Bias-Exchange Metadynamics

Journal of Chemical Theory and Computation ◽

10.1021/acs.jctc.5b00047 ◽

2015 ◽

Vol 11 (6) ◽

pp. 2776-2782 ◽

Cited By ~ 50

Author(s):

Gül H. Zerze ◽

Cayla M. Miller ◽

Daniele Granata ◽

Jeetain Mittal

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Energy Surface ◽

Intrinsically Disordered Protein ◽

Replica Exchange ◽

Free Energy Surface ◽

Replica Exchange Molecular Dynamics ◽

Intrinsically Disordered ◽

Disordered Protein

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The investigation of the secondary structure propensities and free-energy landscapes of peptide ligands by replica exchange molecular dynamics simulations

Molecular Simulation ◽

10.1080/08927022.2013.835486 ◽

2013 ◽

Vol 40 (13) ◽

pp. 1015-1025 ◽

Cited By ~ 2

Author(s):

Kadir Demir ◽

Nesrin Kılıç ◽

Fahriye Ceyda Dudak ◽

İsmail Hakkı Boyacı ◽

Fatih Yaşar

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Secondary Structure ◽

Molecular Dynamics Simulations ◽

Peptide Ligands ◽

Replica Exchange ◽

Energy Landscapes ◽

Replica Exchange Molecular Dynamics ◽

Free Energy Landscapes ◽

Dynamics Simulations

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Free Energy Landscape of a DNA−Carbon Nanotube Hybrid Using Replica Exchange Molecular Dynamics

Nano Letters ◽

10.1021/nl802645d ◽

2009 ◽

Vol 9 (2) ◽

pp. 537-541 ◽

Cited By ~ 135

Author(s):

Robert R. Johnson ◽

Axel Kohlmeyer ◽

A. T. Charlie Johnson ◽

Michael L. Klein

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Carbon Nanotube ◽

Energy Landscape ◽

Replica Exchange ◽

Free Energy Landscape ◽

Replica Exchange Molecular Dynamics

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Reduced Free Energy Perturbation/Hamiltonian Replica Exchange Molecular Dynamics Method with Unbiased Alchemical Thermodynamic Axis

The Journal of Physical Chemistry B ◽

10.1021/acs.jpcb.8b03277 ◽

2018 ◽

Vol 122 (41) ◽

pp. 9435-9442 ◽

Cited By ~ 16

Author(s):

Wei Jiang ◽

Jonathan Thirman ◽

Sunhwan Jo ◽

Benoît Roux

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Method ◽

Replica Exchange ◽

Free Energy Perturbation ◽

Replica Exchange Molecular Dynamics ◽

Hamiltonian Replica Exchange ◽

Energy Perturbation ◽

Dynamics Method

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A Refined Free Energy Perturbation Hamiltonian Replica Exchange Molecular Dynamics Method for Absolute Binding Affinity Predictions

Biophysical Journal ◽

10.1016/j.bpj.2017.11.3639 ◽

2018 ◽

Vol 114 (3) ◽

pp. 675a

Author(s):

Wei Jiang

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Binding Affinity ◽

Molecular Dynamics Method ◽

Replica Exchange ◽

Free Energy Perturbation ◽

Replica Exchange Molecular Dynamics ◽

Hamiltonian Replica Exchange ◽

Energy Perturbation ◽

Dynamics Method

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Free energy surfaces of β-hairpin and α-helical peptides generated by replica exchange molecular dynamics with the AGBNP implicit solvent model

Proteins Structure Function and Bioinformatics ◽

10.1002/prot.20104 ◽

2004 ◽

Vol 56 (2) ◽

pp. 310-321 ◽

Cited By ~ 97

Author(s):

Anthony K. Felts ◽

Yuichi Harano ◽

Emilio Gallicchio ◽

Ronald M. Levy

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Replica Exchange ◽

Implicit Solvent ◽

Helical Peptides ◽

Replica Exchange Molecular Dynamics ◽

Implicit Solvent Model ◽

Solvent Model ◽

Energy Surfaces

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

Journal of Chemical Theory and Computation ◽

10.1021/ct1001768 ◽

2010 ◽

Vol 6 (9) ◽

pp. 2559-2565 ◽

Cited By ~ 159

Author(s):

Wei Jiang ◽

Benoît Roux

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Binding Free Energy ◽

Free Energy Calculations ◽

Replica Exchange ◽

Free Energy Perturbation ◽

Replica Exchange Molecular Dynamics ◽

Hamiltonian Replica Exchange ◽

Binding Free Energy Calculations ◽

Energy Perturbation

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Folding Free-Energy Landscape of α-Synuclein (35–97) Via Replica Exchange Molecular Dynamics

Journal of Chemical Information and Modeling ◽

10.1021/acs.jcim.0c01278 ◽

2020 ◽

Author(s):

Karnesh Jain ◽

Othman Ghribi ◽

Jerome Delhommelle

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Energy Landscape ◽

Replica Exchange ◽

Free Energy Landscape ◽

Replica Exchange Molecular Dynamics ◽

Folding Free Energy

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Free energy surfaces of miniproteins with a ββα motif: Replica exchange molecular dynamics simulation with an implicit solvation model

Proteins Structure Function and Bioinformatics ◽

10.1002/prot.20771 ◽

2005 ◽

Vol 62 (3) ◽

pp. 663-671 ◽

Cited By ~ 30

Author(s):

Soonmin Jang ◽

Eunae Kim ◽

Youngshang Pak

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulation ◽

Dynamics Simulation ◽

Replica Exchange ◽

Implicit Solvation ◽

Solvation Model ◽

Replica Exchange Molecular Dynamics ◽

Implicit Solvation Model ◽

Energy Surfaces

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Computing Alchemical Free Energy Differences with Hamiltonian Replica Exchange Molecular Dynamics (H-REMD) Simulations

Journal of Chemical Theory and Computation ◽

10.1021/ct200153u ◽

2011 ◽

Vol 7 (9) ◽

pp. 2721-2727 ◽

Cited By ~ 44

Author(s):

Yilin Meng ◽

Danial Sabri Dashti ◽

Adrian E. Roitberg

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Replica Exchange ◽

Replica Exchange Molecular Dynamics ◽

Hamiltonian Replica Exchange ◽

Alchemical Free Energy

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