The Development of Replica-Exchange-Based Free-Energy Methods

Christopher J. Woods; Jonathan W. Essex; Michael A. King

doi:10.1021/jp0356620

The Development of Replica-Exchange-Based Free-Energy Methods

The Journal of Physical Chemistry B ◽

10.1021/jp0356620 ◽

2003 ◽

Vol 107 (49) ◽

pp. 13703-13710 ◽

Cited By ~ 132

Author(s):

Christopher J. Woods ◽

Jonathan W. Essex ◽

Michael A. King

Keyword(s):

Free Energy ◽

Replica Exchange ◽

Energy Methods

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

Journal of Chemical Theory and Computation ◽

10.1021/acs.jctc.8b01118 ◽

2018 ◽

Vol 15 (2) ◽

pp. 1265-1277 ◽

Cited By ~ 6

Author(s):

Agastya P. Bhati ◽

Shunzhou Wan ◽

Peter V. Coveney

Keyword(s):

Free Energy ◽

Replica Exchange ◽

Energy Methods ◽

Inhibitor Binding ◽

Protein Mutations ◽

Alchemical Free Energy

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Replica-Exchange-Based Free-Energy Methods

New Algorithms for Macromolecular Simulation - Lecture Notes in Computational Science and Engineering ◽

10.1007/3-540-31618-3_14 ◽

2006 ◽

pp. 251-259 ◽

Cited By ~ 4

Author(s):

Christopher J. Woods ◽

Michael A. King ◽

Jonathan W. Essex

Keyword(s):

Free Energy ◽

Replica Exchange ◽

Energy Methods

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Biasing Potential Replica Exchange Multi-Site λ-Dynamics for Efficient Free Energy Calculations of Protein-Ligand Interactions

Biophysical Journal ◽

10.1016/j.bpj.2014.11.1951 ◽

2015 ◽

Vol 108 (2) ◽

pp. 356a

Author(s):

Kira A. Armacost ◽

Garrett B. Goh ◽

Charles L. Brooks

Keyword(s):

Free Energy ◽

Free Energy Calculations ◽

Replica Exchange ◽

Energy Calculations ◽

Protein Ligand Interactions ◽

Ligand Interactions

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Molecular Dynamics of Apo-Adenylate Kinase: A Distance Replica Exchange Method for the Free Energy of Conformational Fluctuations

The Journal of Physical Chemistry B ◽

10.1021/jp064303c ◽

2006 ◽

Vol 110 (47) ◽

pp. 24121-24137 ◽

Cited By ~ 61

Author(s):

Hongfeng Lou ◽

Robert I. Cukier

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Adenylate Kinase ◽

Replica Exchange ◽

Exchange Method ◽

Replica Exchange Method ◽

Kinase A

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Computing the Liquidus of Binary Monatomic Salt Mixtures with Direct Simulation and Alchemical Free Energy Methods

The Journal of Physical Chemistry A ◽

10.1021/acs.jpca.1c06107 ◽

2021 ◽

Author(s):

Ryan S. DeFever ◽

Edward J. Maginn

Keyword(s):

Free Energy ◽

Energy Methods ◽

Direct Simulation ◽

Salt Mixtures ◽

Alchemical Free Energy

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Evolution of Alchemical Free Energy Methods in Drug Discovery

Journal of Chemical Information and Modeling ◽

10.1021/acs.jcim.0c00547 ◽

2020 ◽

Vol 60 (11) ◽

pp. 5308-5318 ◽

Cited By ~ 1

Author(s):

Lin Frank Song ◽

Kenneth M. Merz

Keyword(s):

Free Energy ◽

Drug Discovery ◽

Energy Methods ◽

Alchemical Free Energy

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06/01870 Free energy methods in molecular simulation

Fuel and Energy Abstracts ◽

10.1016/s0140-6701(06)81876-x ◽

2006 ◽

Vol 47 (4) ◽

pp. 283

Keyword(s):

Free Energy ◽

Molecular Simulation ◽

Energy Methods

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Examining Ion Channel Properties Using Free-Energy Methods

Methods in Enzymology - Biothermodynamics, Part B ◽

10.1016/s0076-6879(09)66007-9 ◽

2009 ◽

pp. 155-177 ◽

Cited By ~ 14

Author(s):

Carmen Domene ◽

Simone Furini

Keyword(s):

Free Energy ◽

Ion Channel ◽

Energy Methods ◽

Ion Channel Properties ◽

Channel Properties

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Determining the water damage resistance of nano-clay modified bitumens using the indirect tensile strength and surface free energy methods

Construction and Building Materials ◽

10.1016/j.conbuildmat.2018.02.011 ◽

2018 ◽

Vol 167 ◽

pp. 391-402 ◽

Cited By ~ 18

Author(s):

Hend Ali Omar ◽

Nur Izzi Md. Yusoff ◽

Halil Ceylan ◽

Irman Abdul Rahman ◽

Zainuddin Sajuri ◽

...

Keyword(s):

Tensile Strength ◽

Free Energy ◽

Surface Free Energy ◽

Indirect Tensile Strength ◽

Energy Methods ◽

Damage Resistance ◽

Nano Clay ◽

Indirect Tensile ◽

Water Damage

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Novel Directions in Free Energy Methods and Applications

Journal of Chemical Information and Modeling ◽

10.1021/acs.jcim.9b01174 ◽

2020 ◽

Vol 60 (1) ◽

pp. 1-5 ◽

Cited By ~ 4

Author(s):

Kira A. Armacost ◽

Sereina Riniker ◽

Zoe Cournia

Keyword(s):

Free Energy ◽

Energy Methods

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