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

The Journal of Chemical Physics ◽

10.1063/1.1472510 ◽

2002 ◽

Vol 116 (20) ◽

pp. 9058-9067 ◽

Author(s):

Hiroaki Fukunishi ◽

Osamu Watanabe ◽

Shoji Takada

Keyword(s):

Protein Structure ◽

Protein Structure Prediction ◽

Structure Prediction ◽

Replica Exchange ◽

Biomolecular Systems ◽

Exchange Method ◽

Hamiltonian Replica Exchange ◽

Efficient Sampling ◽

Replica Exchange Method

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Towerd protein structure prediction : Hydrophobicity replica exchange method

Seibutsu Butsuri ◽

10.2142/biophys.41.s172_1 ◽

2001 ◽

Vol 41 (supplement) ◽

pp. S172

Author(s):

H Fukunishi ◽

O Watanabe ◽

S Takada

Keyword(s):

Protein Structure ◽

Protein Structure Prediction ◽

Structure Prediction ◽

Replica Exchange ◽

Exchange Method ◽

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 ◽

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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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 ◽

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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Efficient Sampling in Fragment-Based Protein Structure Prediction Using an Estimation of Distribution Algorithm

PLoS ONE ◽

10.1371/journal.pone.0068954 ◽

2013 ◽

Vol 8 (7) ◽

pp. e68954 ◽

Author(s):

David Simoncini ◽

Kam Y. J. Zhang

Keyword(s):

Protein Structure ◽

Protein Structure Prediction ◽

Structure Prediction ◽

Estimation Of Distribution Algorithm ◽

Efficient Sampling ◽

Estimation Of Distribution

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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 ◽

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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De Novo Protein Structure Prediction by Combining Replica Exchange Simulations with Coevolutionary Data

Biophysical Journal ◽

10.1016/j.bpj.2017.11.3138 ◽

2018 ◽

Vol 114 (3) ◽

pp. 574a

Author(s):

Arthur Voronin ◽

Alexander Schug

Keyword(s):

Protein Structure ◽

Protein Structure Prediction ◽

Structure Prediction ◽

De Novo ◽

Replica Exchange

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4013 Protein Structure Analysis using Fast Multipole Method and Replica-exchange Method

The Proceedings of The Computational Mechanics Conference ◽

10.1299/jsmecmd.2005.18.239 ◽

2005 ◽

Vol 2005.18 (0) ◽

pp. 239-240

Author(s):

Masaaki SUZUKI ◽

Hiroshi OKUDA

Keyword(s):

Protein Structure ◽

Structure Analysis ◽

Fast Multipole Method ◽

Replica Exchange ◽

Fast Multipole ◽

Protein Structure Analysis ◽

Exchange Method ◽

Multipole Method ◽

Replica Exchange Method

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A Hamiltonian replica exchange method for building protein–protein interfaces applied to a leucine zipper

The Journal of Chemical Physics ◽

10.1063/1.3548074 ◽

2011 ◽

Vol 134 (4) ◽

pp. 045104 ◽

Author(s):

Robert I. Cukier

Keyword(s):

Leucine Zipper ◽

Replica Exchange ◽

Exchange Method ◽

Hamiltonian Replica Exchange ◽

Protein Interfaces ◽

Replica Exchange Method

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A population-based conformational optimal algorithm using replica-exchange in ab-initio protein structure prediction

2016 Chinese Control and Decision Conference (CCDC) ◽

10.1109/ccdc.2016.7531076 ◽

2016 ◽

Author(s):

Guijun Zhang ◽

Xufeng Yu ◽

Xiaogen Zhou ◽

Xiaohu Hao

Keyword(s):

Protein Structure ◽

Ab Initio ◽

Protein Structure Prediction ◽

Structure Prediction ◽

Optimal Algorithm ◽

Population Based ◽

Replica Exchange

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Protein structure prediction with the UNRES force-field using Replica-Exchange Monte Carlo-with-Minimization; Comparison with MCM, CSA, and CFMC

Journal of Computational Chemistry ◽

10.1002/jcc.20286 ◽

2005 ◽

Vol 26 (14) ◽

pp. 1472-1486 ◽

Author(s):

Marian Nanias ◽

Maurizio Chinchio ◽

Stanisław Ołdziej ◽

Cezary Czaplewski ◽

Harold A. Scheraga

Keyword(s):

Monte Carlo ◽

Protein Structure ◽

Force Field ◽

Protein Structure Prediction ◽

Structure Prediction ◽

Replica Exchange ◽

Replica Exchange Monte Carlo

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