Multidimensional replica-exchange method for free-energy calculations

Yuji Sugita; Akio Kitao; Yuko Okamoto

doi:10.1063/1.1308516

Multidimensional replica-exchange method for free-energy calculations

The Journal of Chemical Physics ◽

10.1063/1.1308516 ◽

2000 ◽

Vol 113 (15) ◽

pp. 6042-6051 ◽

Cited By ~ 575

Author(s):

Yuji Sugita ◽

Akio Kitao ◽

Yuko Okamoto

Keyword(s):

Free Energy ◽

Free Energy Calculations ◽

Replica Exchange ◽

Exchange Method ◽

Energy Calculations ◽

Replica Exchange Method

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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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Minimizing thermodynamic length to select intermediate states for free-energy calculations and replica-exchange simulations

Physical Review E ◽

10.1103/physreve.80.046705 ◽

2009 ◽

Vol 80 (4) ◽

Cited By ~ 42

Author(s):

Daniel K. Shenfeld ◽

Huafeng Xu ◽

Michael P. Eastwood ◽

Ron O. Dror ◽

David E. Shaw

Keyword(s):

Free Energy ◽

Free Energy Calculations ◽

Replica Exchange ◽

Energy Calculations ◽

Intermediate States

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Satisfying the fluctuation theorem in free-energy calculations with Hamiltonian replica exchange

Physical Review E ◽

10.1103/physreve.77.026104 ◽

2008 ◽

Vol 77 (2) ◽

Cited By ~ 5

Author(s):

Matthew A. Wyczalkowski ◽

Rohit V. Pappu

Keyword(s):

Free Energy ◽

Free Energy Calculations ◽

Fluctuation Theorem ◽

Replica Exchange ◽

Energy Calculations ◽

Hamiltonian Replica Exchange

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Publisher's Note: Minimizing thermodynamic length to select intermediate states for free-energy calculations and replica-exchange simulations [Phys. Rev. E80, 046705 (2009)]

Physical Review E ◽

10.1103/physreve.80.049904 ◽

2009 ◽

Vol 80 (4) ◽

Cited By ~ 1

Author(s):

Daniel K. Shenfeld ◽

Huafeng Xu ◽

Michael P. Eastwood ◽

Ron O. Dror ◽

David E. Shaw

Keyword(s):

Free Energy ◽

Free Energy Calculations ◽

Replica Exchange ◽

Energy Calculations ◽

Intermediate States

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Free energy calculations of DNA base stacking using Replica-Exchange Umbrella Sampling

Seibutsu Butsuri ◽

10.2142/biophys.43.s89_1 ◽

2003 ◽

Vol 43 (supplement) ◽

pp. S89

Author(s):

K. Murata ◽

Y. Sugita ◽

Y. Okamoto

Keyword(s):

Free Energy ◽

Umbrella Sampling ◽

Free Energy Calculations ◽

Replica Exchange ◽

Base Stacking ◽

Energy Calculations ◽

Dna Base

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Exploring the protein folding free energy landscape: coupling replica exchange method with P3ME/RESPA algorithm

Journal of Molecular Graphics and Modelling ◽

10.1016/j.jmgm.2003.12.011 ◽

2004 ◽

Vol 22 (5) ◽

pp. 451-463 ◽

Cited By ~ 52

Author(s):

Ruhong Zhou

Keyword(s):

Free Energy ◽

Protein Folding ◽

Energy Landscape ◽

Replica Exchange ◽

Free Energy Landscape ◽

Exchange Method ◽

Replica Exchange Method ◽

Folding Free Energy

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Comment on `Free energy calculations for DNA base stacking by replica-exchange umbrella sampling' by Katsumi Murata, Yuji Sugita, Yuko Okamoto

Chemical Physics Letters ◽

10.1016/j.cplett.2004.06.046 ◽

2004 ◽

Vol 393 (1-3) ◽

pp. 282-283 ◽

Cited By ~ 2

Author(s):

Jan Norberg ◽

Lennart Nilsson

Keyword(s):

Free Energy ◽

Umbrella Sampling ◽

Free Energy Calculations ◽

Replica Exchange ◽

Base Stacking ◽

Energy Calculations ◽

Dna Base

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Free energy calculations of the stacked and unstacked states for DNA dimers by replica-exchange umbrella sampling

10.1063/1.1764161 ◽

2004 ◽

Author(s):

Katsumi Murata

Keyword(s):

Free Energy ◽

Umbrella Sampling ◽

Free Energy Calculations ◽

Replica Exchange ◽

Energy Calculations

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Publisher's Note: Satisfying the fluctuation theorem in free-energy calculations with Hamiltonian replica exchange [Phys. Rev. E77, 026104 (2008)]

Physical Review E ◽

10.1103/physreve.77.029905 ◽

2008 ◽

Vol 77 (2) ◽

Author(s):

Matthew A. Wyczalkowski ◽

Rohit V. Pappu

Keyword(s):

Free Energy ◽

Free Energy Calculations ◽

Fluctuation Theorem ◽

Replica Exchange ◽

Energy Calculations ◽

Hamiltonian Replica Exchange

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