1PT131 Development and application of the helix-strand replica-exchange molecular dynamics method(The 50th Annual Meeting of the Biophysical Society of Japan)

Replica Exchange ◽

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 ◽

Replica Exchange ◽

Efficient Sampling ◽

Biophysical Society ◽

1P321 Mass-scaling replica-exchange molecular dynamics method(30. Miscellaneous topics,Poster,The 52nd Annual Meeting of the Biophysical Society of Japan(BSJ2014))

Seibutsu Butsuri ◽

10.2142/biophys.54.s194_3 ◽

2014 ◽

Vol 54 (supplement1-2) ◽

pp. S194

Author(s):

Tetsuro Nagai ◽

Takuya Takahashi

Keyword(s):

Molecular Dynamics ◽

Annual Meeting ◽

Replica Exchange ◽

Mass Scaling ◽

Biophysical Society ◽

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 ◽

Biophysical Society ◽

Dynamics Simulations

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 ◽

Replica Exchange ◽

Conformational Sampling ◽

Membrane Systems ◽

Protein Folding with the Parallel Replica Exchange Molecular Dynamics Method

Parallel Computing for Bioinformatics and Computational Biology ◽

10.1002/0471756504.ch17 ◽

2005 ◽

pp. 395-425

Author(s):

Ruhong Zhou

Keyword(s):

Molecular Dynamics ◽

Protein Folding ◽

Replica Exchange ◽

3P077 Refinement of Modeled Protein Structure by Replica Exchange Molecular Dynamics and Hydration Entropy based Scoring Function(Protein: Property,The 48th Annual Meeting of the Biophysical Society of Japan)

Seibutsu Butsuri ◽

10.2142/biophys.50.s158_3 ◽

2010 ◽

Vol 50 (supplement2) ◽

pp. S158

Author(s):

Shiqiao Du ◽

Yuichi Harano ◽

Minoru Sakurai ◽

Masahiro Kinoshita

Keyword(s):

Molecular Dynamics ◽

Protein Structure ◽

Annual Meeting ◽

Scoring Function ◽

Replica Exchange ◽

Protein Property ◽

Biophysical Society

Reduced Free Energy Perturbation/Hamiltonian Replica Exchange Molecular Dynamics Method with Unbiased Alchemical Thermodynamic Axis

The Journal of Physical Chemistry B ◽

10.1021/acs.jpcb.8b03277 ◽

2018 ◽

Vol 122 (41) ◽

pp. 9435-9442 ◽

Cited By ~ 16

Author(s):

Wei Jiang ◽

Jonathan Thirman ◽

Sunhwan Jo ◽

Benoît Roux

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Replica Exchange ◽

Free Energy Perturbation ◽

Hamiltonian Replica Exchange ◽

Energy Perturbation ◽

A Refined Free Energy Perturbation Hamiltonian Replica Exchange Molecular Dynamics Method for Absolute Binding Affinity Predictions

Biophysical Journal ◽

10.1016/j.bpj.2017.11.3639 ◽

2018 ◽

Vol 114 (3) ◽

pp. 675a

Author(s):

Wei Jiang

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Binding Affinity ◽

Replica Exchange ◽

Free Energy Perturbation ◽

Hamiltonian Replica Exchange ◽

Energy Perturbation ◽

1TP3-05 Characterization of monomeric polyglutamine peptides by replica exchange molecular dynamics simulation(The 47th Annual Meeting of the Biophysical Society of Japan)

Seibutsu Butsuri ◽

10.2142/biophys.49.s34_6 ◽

2009 ◽

Vol 49 (supplement) ◽

pp. S34-S35

Author(s):

Miki Nakano ◽

Hirofumi Watanabe ◽

Shigenori Tanaka

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Annual Meeting ◽

Dynamics Simulation ◽

Replica Exchange ◽

Biophysical Society

3P044 The development of multi-dimensional replica-exchange molecular dynamics program (REIN)(Protein: Structure & Function,The 48th Annual Meeting of the Biophysical Society of Japan)

Seibutsu Butsuri ◽

10.2142/biophys.50.s152_5 ◽

2010 ◽

Vol 50 (supplement2) ◽

pp. S152-S153

Author(s):

Naoyuki Miyashita ◽

Mitsunori Ikeguchi ◽

Yuji Sugita

Keyword(s):

Molecular Dynamics ◽

Protein Structure ◽

Structure Function ◽

Annual Meeting ◽

Replica Exchange ◽

Biophysical Society