Two-dimensional replica-exchange method for predicting protein-ligand binding structures

Hironori Kokubo; Toshimasa Tanaka; Yuko Okamoto

doi:10.1002/jcc.23427

Two-dimensional replica-exchange method for predicting protein-ligand binding structures

Journal of Computational Chemistry ◽

10.1002/jcc.23427 ◽

2013 ◽

Vol 34 (30) ◽

pp. 2601-2614 ◽

Cited By ~ 27

Author(s):

Hironori Kokubo ◽

Toshimasa Tanaka ◽

Yuko Okamoto

Keyword(s):

Ligand Binding ◽

Replica Exchange ◽

Two Dimensional ◽

Exchange Method ◽

Replica Exchange Method

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Prediction of Ligand Binding Affinity by the Combination of Replica-Exchange Method and Double-Decoupling Method

Journal of Chemical Theory and Computation ◽

10.1021/ct500539u ◽

2014 ◽

Vol 10 (8) ◽

pp. 3563-3569 ◽

Cited By ~ 7

Author(s):

Yuko Okamoto ◽

Hironori Kokubo ◽

Toshimasa Tanaka

Keyword(s):

Ligand Binding ◽

Binding Affinity ◽

Replica Exchange ◽

Exchange Method ◽

Decoupling Method ◽

Replica Exchange Method

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Enhancing Constant-pH Simulation in Explicit Solvent with a Two-Dimensional Replica Exchange Method

Journal of Chemical Theory and Computation ◽

10.1021/ct501101f ◽

2015 ◽

Vol 11 (6) ◽

pp. 2560-2574 ◽

Cited By ~ 23

Author(s):

Juyong Lee ◽

Benjamin T. Miller ◽

Ana Damjanović ◽

Bernard R. Brooks

Keyword(s):

Replica Exchange ◽

Two Dimensional ◽

Exchange Method ◽

Constant Ph ◽

Explicit Solvent ◽

Replica Exchange Method

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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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Hamiltonian Replica Exchange Method Study of Escherichia coli and Yersinia pestis HPPK

The Journal of Physical Chemistry B ◽

10.1021/jp903861a ◽

2009 ◽

Vol 113 (50) ◽

pp. 16197-16208 ◽

Cited By ~ 5

Author(s):

Li Su ◽

Robert I. Cukier

Keyword(s):

Escherichia Coli ◽

Yersinia Pestis ◽

Replica Exchange ◽

Exchange Method ◽

Hamiltonian Replica Exchange ◽

Replica Exchange Method

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Hamiltonian and Distance Replica Exchange Method Studies of Met-Enkephalin

The Journal of Physical Chemistry B ◽

10.1021/jp073314i ◽

2007 ◽

Vol 111 (42) ◽

pp. 12310-12321 ◽

Cited By ~ 13

Author(s):

Li Su ◽

Robert I. Cukier

Keyword(s):

Replica Exchange ◽

Exchange Method ◽

Replica Exchange Method

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Hamiltonian Replica Exchange Method Studies of a Leucine Zipper Dimer

The Journal of Physical Chemistry B ◽

10.1021/jp900309q ◽

2009 ◽

Vol 113 (28) ◽

pp. 9595-9605 ◽

Cited By ~ 11

Author(s):

Li Su ◽

Robert I. Cukier

Keyword(s):

Leucine Zipper ◽

Replica Exchange ◽

Exchange Method ◽

Hamiltonian Replica Exchange ◽

Replica Exchange Method

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Efficient sampling of ion motions in molecular dynamics simulations on DNA: Variant Hamiltonian replica exchange method

Chemical Physics Letters ◽

10.1016/j.cplett.2008.02.055 ◽

2008 ◽

Vol 454 (4-6) ◽

pp. 391-395 ◽

Cited By ~ 13

Author(s):

Donghong Min ◽

Hongzhi Li ◽

Guohui Li ◽

Bernd A. Berg ◽

Marcia O. Fenley ◽

...

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Replica Exchange ◽

Exchange Method ◽

Hamiltonian Replica Exchange ◽

Efficient Sampling ◽

Dynamics Simulations ◽

Replica Exchange Method

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Replica-exchange method using Tsallis statistics for protein folding

Seibutsu Butsuri ◽

10.2142/biophys.40.s165_2 ◽

2000 ◽

Vol 40 (supplement) ◽

pp. S165

Author(s):

M. Ito ◽

Y. Okamoto

Keyword(s):

Protein Folding ◽

Replica Exchange ◽

Exchange Method ◽

Tsallis Statistics ◽

Replica Exchange Method

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A convective replica-exchange method for sampling new energy basins

Journal of Computational Chemistry ◽

10.1002/jcc.23113 ◽

2012 ◽

Vol 34 (2) ◽

pp. 132-140 ◽

Cited By ~ 16

Author(s):

Yannick G. Spill ◽

Guillaume Bouvier ◽

Michael Nilges

Keyword(s):

Replica Exchange ◽

Exchange Method ◽

New Energy ◽

Replica Exchange Method

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Replica-Permutation Method with the Suwa–Todo Algorithm beyond the Replica-Exchange Method

Journal of Chemical Theory and Computation ◽

10.1021/ct3007919 ◽

2012 ◽

Vol 9 (1) ◽

pp. 570-581 ◽

Cited By ~ 52

Author(s):

Satoru G. Itoh ◽

Hisashi Okumura

Keyword(s):

Replica Exchange ◽

Exchange Method ◽

Replica Exchange Method

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