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)

Annual Meeting ◽

Replica Exchange ◽

Biophysical Society ◽

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 ◽

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 ◽

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 ◽

1P242 1I1435 Analysis of the effect of water molecules on lipid bilayer dynamics in aqueous salt solutions using molecular dynamics simulations(Biol & Artifi memb.:Dynamics,Oral Presentations,The 48th Annual Meeting of the Biophysical Society of Japan)

Seibutsu Butsuri ◽

10.2142/biophys.50.s62_2 ◽

2010 ◽

Vol 50 (supplement2) ◽

pp. S62

Author(s):

Rina Kagawa ◽

Yoshinori Hirano ◽

Kenji Yasuoka ◽

Masato Yasui

Keyword(s):

Molecular Dynamics ◽

Annual Meeting ◽

Lipid Bilayer ◽

Water Molecules ◽

Salt Solutions ◽

Aqueous Salt Solutions ◽

Biophysical Society ◽

Dynamics Simulations ◽

Oral Presentations

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 ◽

1P-030 Analysis of Tension Sensing Sites of E-coli Mechanosensitive Channel MscL Using Molecular Dynamics Simulations(The 46th Annual Meeting of the Biophysical Society of Japan)

Seibutsu Butsuri ◽

10.2142/biophys.48.s25_4 ◽

2008 ◽

Vol 48 (supplement) ◽

pp. S25

Author(s):

Yasuyuki Sawada ◽

Masaki Murase ◽

Masahiro Sokabe

Keyword(s):

Molecular Dynamics ◽

Annual Meeting ◽

Mechanosensitive Channel ◽

E Coli ◽

Biophysical Society ◽

3B1010 Molecular dynamics simulations of dynein motor domain in explicit water(Proteins:Structure & Function III:Dynamics and Circadian Rhythm,Oral Presentation,The 50th Annual Meeting of the Biophysical Society of Japan)

Seibutsu Butsuri ◽

10.2142/biophys.52.s58_4 ◽

2012 ◽

Vol 52 (supplement) ◽

pp. S58

Author(s):

Narutoshi Kamiya ◽

Tadaaki Mashimo ◽

Yu Takano ◽

Takahide Kon ◽

Genji Kurisu ◽

...

Keyword(s):

Molecular Dynamics ◽

Circadian Rhythm ◽

Annual Meeting ◽

Oral Presentation ◽

Motor Domain ◽

Dynein Motor ◽

Biophysical Society ◽

Dynamics Simulations ◽

Explicit Water

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 ◽

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 ◽

Replica Exchange ◽

Loop Structure ◽

Hairpin Loop ◽

Dna Hairpin ◽

Explicit Solvent ◽