Hamiltonian replica exchange combined with elastic network analysis to enhance global domain motions in atomistic molecular dynamics simulations

Katja Ostermeir; Martin Zacharias

doi:10.1002/prot.24695

Hamiltonian replica exchange combined with elastic network analysis to enhance global domain motions in atomistic molecular dynamics simulations

Proteins Structure Function and Bioinformatics ◽

10.1002/prot.24695 ◽

2014 ◽

Vol 82 (12) ◽

pp. 3410-3419 ◽

Cited By ~ 8

Author(s):

Katja Ostermeir ◽

Martin Zacharias

Keyword(s):

Molecular Dynamics ◽

Network Analysis ◽

Molecular Dynamics Simulations ◽

Replica Exchange ◽

Elastic Network ◽

Hamiltonian Replica Exchange ◽

Dynamics Simulations ◽

Domain Motions

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Combining Elastic Network Analysis and Molecular Dynamics Simulations by Hamiltonian Replica Exchange

Journal of Chemical Theory and Computation ◽

10.1021/ct7002258 ◽

2008 ◽

Vol 4 (3) ◽

pp. 477-487 ◽

Cited By ~ 32

Author(s):

Martin Zacharias

Keyword(s):

Molecular Dynamics ◽

Network Analysis ◽

Molecular Dynamics Simulations ◽

Replica Exchange ◽

Elastic Network ◽

Hamiltonian Replica Exchange ◽

Dynamics Simulations

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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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Mimicking the action of folding chaperones by Hamiltonian replica-exchange molecular dynamics simulations: Application in the refinement of de novo models

Proteins Structure Function and Bioinformatics ◽

10.1002/prot.24068 ◽

2012 ◽

Vol 80 (7) ◽

pp. 1744-1754 ◽

Cited By ~ 10

Author(s):

Hao Fan ◽

Xavier Periole ◽

Alan E. Mark

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

De Novo ◽

Replica Exchange ◽

Replica Exchange Molecular Dynamics ◽

Hamiltonian Replica Exchange ◽

Dynamics Simulations

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Plasticity of 150-Loop in Influenza Neuraminidase Explored by Hamiltonian Replica Exchange Molecular Dynamics Simulations

PLoS ONE ◽

10.1371/journal.pone.0060995 ◽

2013 ◽

Vol 8 (4) ◽

pp. e60995 ◽

Cited By ~ 15

Author(s):

Nanyu Han ◽

Yuguang Mu

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Replica Exchange ◽

Replica Exchange Molecular Dynamics ◽

Hamiltonian Replica Exchange ◽

Dynamics Simulations

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Molecular Dynamics Simulations and Elastic Network Analysis of Protein Kinase B (Akt/PKB) Inactivation

Journal of Chemical Information and Modeling ◽

10.1021/ci100076j ◽

2010 ◽

Vol 50 (9) ◽

pp. 1602-1610 ◽

Cited By ~ 23

Author(s):

Shu Cheng ◽

Masha Y. Niv

Keyword(s):

Molecular Dynamics ◽

Protein Kinase ◽

Network Analysis ◽

Molecular Dynamics Simulations ◽

Protein Kinase B ◽

Elastic Network ◽

Dynamics Simulations

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Ergodicity and model quality in template-restrained canonical and temperature/Hamiltonian replica exchange coarse-grained molecular dynamics simulations of proteins

Journal of Computational Chemistry ◽

10.1002/jcc.25070 ◽

2017 ◽

Vol 38 (31) ◽

pp. 2730-2746 ◽

Cited By ~ 3

Author(s):

Agnieszka S. Karczyńska ◽

Cezary Czaplewski ◽

Paweł Krupa ◽

Magdalena A. Mozolewska ◽

Keehyoung Joo ◽

...

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Coarse Grained ◽

Replica Exchange ◽

Model Quality ◽

Hamiltonian Replica Exchange ◽

Dynamics Simulations ◽

Coarse Grained Molecular Dynamics

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Faculty Opinions recommendation of Mechanism of intracellular block of the KcsA K+ channel by tetrabutylammonium: insights from X-ray crystallography, electrophysiology and replica-exchange molecular dynamics simulations.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1048003.498039 ◽

2006 ◽

Author(s):

D Peter Tieleman

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Replica Exchange ◽

K Channel ◽

Replica Exchange Molecular Dynamics ◽

X Ray ◽

X Ray Crystallography ◽

Dynamics Simulations

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Calculation of Protein Heat Capacity from Replica-Exchange Molecular Dynamics Simulations with Different Implicit Solvent Models

The Journal of Physical Chemistry B ◽

10.1021/jp802469g ◽

2008 ◽

Vol 112 (47) ◽

pp. 15064-15073 ◽

Cited By ~ 33

Author(s):

In-Chul Yeh ◽

Michael S. Lee ◽

Mark A. Olson

Keyword(s):

Molecular Dynamics ◽

Heat Capacity ◽

Molecular Dynamics Simulations ◽

Replica Exchange ◽

Implicit Solvent ◽

Replica Exchange Molecular Dynamics ◽

Solvent Models ◽

Dynamics Simulations ◽

Implicit Solvent Models

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3P314 Conformational analysis of PA-glycans by replica-exchange molecular dynamics simulations(30.Miscellaneous topics,Poster,The 51st Annual Meeting of the Biophysical Society of Japan)

Seibutsu Butsuri ◽

10.2142/biophys.53.s264_1 ◽

2013 ◽

Vol 53 (supplement1-2) ◽

pp. S264

Author(s):

Shigehisa Watanabe ◽

Suyong Re ◽

Eiro Muneyuki ◽

Yuji Sugita

Keyword(s):

Molecular Dynamics ◽

Conformational Analysis ◽

Molecular Dynamics Simulations ◽

Annual Meeting ◽

Replica Exchange ◽

Replica Exchange Molecular Dynamics ◽

Biophysical Society ◽

Dynamics Simulations

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Insights into the Folding and Unfolding Processes of Wild-Type and Mutated SH3 Domain by Molecular Dynamics and Replica Exchange Molecular Dynamics Simulations

PLoS ONE ◽

10.1371/journal.pone.0064886 ◽

2013 ◽

Vol 8 (5) ◽

pp. e64886 ◽

Cited By ~ 6

Author(s):

Wen-Ting Chu ◽

Ji-Long Zhang ◽

Qing-Chuan Zheng ◽

Lin Chen ◽

Hong-Xing Zhang

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Sh3 Domain ◽

Replica Exchange ◽

Wild Type ◽

Replica Exchange Molecular Dynamics ◽

Dynamics Simulations

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