1P216 Surface-tension replica-exchange molecular dynamics simulations of biological membrane systems(13B. Biological & Artificial membrane: Dynamics,Poster,The 52nd Annual Meeting of the Biophysical Society of Japan(BSJ2014))

Biophysical Society ◽

Surface-Tension Replica-Exchange Molecular Dynamics Method for Efficient Conformational Sampling of Biological Membrane Systems

Biophysical Journal ◽

10.1016/j.bpj.2013.11.3894 ◽

2014 ◽

Vol 106 (2) ◽

pp. 704a ◽

Cited By ~ 1

Author(s):

Takaharu Mori ◽

Jaewoon Jung ◽

Yuji Sugita

Keyword(s):

Molecular Dynamics ◽

Surface Tension ◽

Biological Membrane ◽

Molecular Dynamics Method ◽

Replica Exchange ◽

Conformational Sampling ◽

Membrane Systems ◽

Dynamics Method

2P-172 Replica-exchange molecular dynamics simulations of membrane systems(Biol & Artifi memb.:Structure & Property,The 47th Annual Meeting of the Biophysical Society of Japan)

Seibutsu Butsuri ◽

10.2142/biophys.49.s133_5 ◽

2009 ◽

Vol 49 (supplement) ◽

pp. S133

Author(s):

Tetsuro Nagai ◽

Yuko Okamoto

Keyword(s):

Molecular Dynamics ◽

Annual Meeting ◽

Replica Exchange ◽

Structure Property ◽

Membrane Systems ◽

Biophysical Society ◽

Surface-Tension Replica-Exchange Molecular Dynamics Method for Enhanced Sampling of Biological Membrane Systems

Journal of Chemical Theory and Computation ◽

10.1021/ct400445k ◽

2013 ◽

Vol 9 (12) ◽

pp. 5629-5640 ◽

Cited By ~ 29

Author(s):

Takaharu Mori ◽

Jaewoon Jung ◽

Yuji Sugita

Keyword(s):

Molecular Dynamics ◽

Surface Tension ◽

Biological Membrane ◽

Molecular Dynamics Method ◽

Replica Exchange ◽

Enhanced Sampling ◽

Membrane Systems ◽

Dynamics Method

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 ◽

Annual Meeting ◽

Replica Exchange ◽

Biophysical Society ◽

3D0936 Prediction of dynamical conformation of biantennary complex-type N-glycan in water by replica-exchange molecular dynamics simulations(3D Protein: Structure & Function 2,The 49th Annual Meeting of the Biophysical Society of Japan)

Seibutsu Butsuri ◽

10.2142/biophys.51.s117_3 ◽

2011 ◽

Vol 51 (supplement) ◽

pp. S117

Author(s):

Suyong Re ◽

Naoyuki Miyashita ◽

Yoshiki Yamaguchi ◽

Yuji Sugita

Keyword(s):

Molecular Dynamics ◽

Protein Structure ◽

Structure Function ◽

Replica Exchange ◽

Complex Type ◽

3D Protein Structure ◽

Biophysical Society ◽

3PT157 Surface tension replica exchange molecular dynamics method for an efficient sampling of lipid bilayer structures(The 50th Annual Meeting of the Biophysical Society of Japan)

Seibutsu Butsuri ◽

10.2142/biophys.52.s168_1 ◽

2012 ◽

Vol 52 (supplement) ◽

pp. S168

Author(s):

Takaharu Mori ◽

Yuji Sugita

Keyword(s):

Molecular Dynamics ◽

Surface Tension ◽

Annual Meeting ◽

Lipid Bilayer ◽

Molecular Dynamics Method ◽

Replica Exchange ◽

Efficient Sampling ◽

Biophysical Society ◽

Dynamics Method

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 ◽

Replica Exchange ◽

K Channel ◽

X Ray ◽

X Ray Crystallography ◽

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 ◽

Replica Exchange ◽

Implicit Solvent ◽

Solvent Models ◽

Dynamics Simulations ◽

Implicit Solvent Models

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 ◽

Sh3 Domain ◽

Replica Exchange ◽

Wild Type ◽

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 ◽

Force Fields ◽

Dynamic Properties ◽

Amyloid Β ◽

Replica Exchange ◽