Reliable Oligonucleotide Conformational Ensemble Generation in Explicit Solvent for Force Field Assessment Using Reservoir Replica Exchange Molecular Dynamics Simulations

Niel M. Henriksen; Daniel R. Roe; Thomas E. Cheatham

doi:10.1021/jp400530e

Reliable Oligonucleotide Conformational Ensemble Generation in Explicit Solvent for Force Field Assessment Using Reservoir Replica Exchange Molecular Dynamics Simulations

The Journal of Physical Chemistry B ◽

10.1021/jp400530e ◽

2013 ◽

Vol 117 (15) ◽

pp. 4014-4027 ◽

Cited By ~ 45

Author(s):

Niel M. Henriksen ◽

Daniel R. Roe ◽

Thomas E. Cheatham

Keyword(s):

Molecular Dynamics ◽

Force Field ◽

Molecular Dynamics Simulations ◽

Replica Exchange ◽

Conformational Ensemble ◽

Replica Exchange Molecular Dynamics ◽

Explicit Solvent ◽

Field Assessment ◽

Dynamics Simulations ◽

Ensemble Generation

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Folding of a DNA Hairpin Loop Structure in Explicit Solvent Using Replica-Exchange Molecular Dynamics Simulations

Biophysical Journal ◽

10.1529/biophysj.107.108019 ◽

2007 ◽

Vol 93 (9) ◽

pp. 3218-3228 ◽

Cited By ~ 40

Author(s):

Srinivasaraghavan Kannan ◽

Martin Zacharias

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Replica Exchange ◽

Loop Structure ◽

Hairpin Loop ◽

Dna Hairpin ◽

Replica Exchange Molecular Dynamics ◽

Explicit Solvent ◽

Dynamics Simulations

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The Structure of the Alzheimer Amyloid β 10-35 Peptide Probed through Replica-Exchange Molecular Dynamics Simulations in Explicit Solvent

Journal of Molecular Biology ◽

10.1016/j.jmb.2006.11.015 ◽

2007 ◽

Vol 366 (1) ◽

pp. 275-285 ◽

Cited By ~ 102

Author(s):

Andrij Baumketner ◽

Joan-Emma Shea

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Amyloid Β ◽

Replica Exchange ◽

Replica Exchange Molecular Dynamics ◽

Explicit Solvent ◽

Dynamics Simulations

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Folding simulations of Trp-cage mini protein in explicit solvent using biasing potential replica-exchange molecular dynamics simulations

Proteins Structure Function and Bioinformatics ◽

10.1002/prot.22359 ◽

2008 ◽

Vol 76 (2) ◽

pp. 448-460 ◽

Cited By ~ 46

Author(s):

Srinivasaraghavan Kannan ◽

Martin Zacharias

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Replica Exchange ◽

Replica Exchange Molecular Dynamics ◽

Explicit Solvent ◽

Folding Simulations ◽

Dynamics Simulations

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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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Effects of force fields on the conformational and dynamic properties of amyloid β(1-40) dimer explored by replica exchange molecular dynamics simulations

Proteins Structure Function and Bioinformatics ◽

10.1002/prot.25439 ◽

2017 ◽

Vol 86 (3) ◽

pp. 279-300 ◽

Cited By ~ 13

Author(s):

Charles R. Watts ◽

Andrew Gregory ◽

Cole Frisbie ◽

Sándor Lovas

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Force Fields ◽

Dynamic Properties ◽

Amyloid Β ◽

Replica Exchange ◽

Replica Exchange Molecular Dynamics ◽

Dynamics Simulations

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Understanding the folding and stability of a designed WW domain protein with replica exchange molecular dynamics simulations

Molecular Simulation ◽

10.1080/08927022.2013.773431 ◽

2013 ◽

Vol 39 (10) ◽

pp. 828-836 ◽

Cited By ~ 4

Author(s):

Jian-ping Hu ◽

Hong-qiu He ◽

Xiong Jiao ◽

Shan Chang

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Replica Exchange ◽

Ww Domain ◽

Replica Exchange Molecular Dynamics ◽

Domain Protein ◽

Dynamics Simulations

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Reconstructing the Most Probable Folding Transition Path from Replica Exchange Molecular Dynamics Simulations

Journal of Chemical Theory and Computation ◽

10.1021/ct400170x ◽

2013 ◽

Vol 9 (8) ◽

pp. 3750-3755 ◽

Cited By ~ 2

Author(s):

Camilo Andres Jimenez-Cruz ◽

Angel E. Garcia

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Replica Exchange ◽

Transition Path ◽

Replica Exchange Molecular Dynamics ◽

Dynamics Simulations

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