3P107 Molecular dynamics simulations of β2AR : the comparison of different protein-lipid force field parameters(03. Membrane proteins,Poster,The 52nd Annual Meeting of the Biophysical Society of Japan(BSJ2014))

Annual Meeting ◽

Biophysical Society ◽

Force Field Parameters ◽

1P105 Molecular dynamics simulations of ATP/ADP bound forms of SR Ca^-ATPase using CHARMM force field with modified polyphosphate parameters(03. Membrane proteins,Poster,The 52nd Annual Meeting of the Biophysical Society of Japan(BSJ2014))

Seibutsu Butsuri ◽

10.2142/biophys.54.s158_3 ◽

2014 ◽

Vol 54 (supplement1-2) ◽

pp. S158

Author(s):

Yasuaki Komuro ◽

Suyong Re ◽

Chigusa Kobayashi ◽

Eiro Muneyuki ◽

Yuji Sugita

Keyword(s):

Molecular Dynamics ◽

Membrane Proteins ◽

Force Field ◽

Annual Meeting ◽

Biophysical Society ◽

Charmm Force Field ◽

1B1648 All-atom molecular dynamics simulations of drug efflux transporter AcrB(Membrane Proteins 1,The 49th Annual Meeting of the Biophysical Society of Japan)

Seibutsu Butsuri ◽

10.2142/biophys.51.s33_4 ◽

2011 ◽

Vol 51 (supplement) ◽

pp. S33

Author(s):

Tsutomu Yamane ◽

Mitsunori Ikeguchi

Keyword(s):

Molecular Dynamics ◽

Membrane Proteins ◽

Annual Meeting ◽

Drug Efflux ◽

Efflux Transporter ◽

Biophysical Society ◽

1B1624 Molecular dynamics simulations of SRII-HtrII complex with a modeled HAMP domain(Membrane Proteins 1,The 49th Annual Meeting of the Biophysical Society of Japan)

Seibutsu Butsuri ◽

10.2142/biophys.51.s33_2 ◽

2011 ◽

Vol 51 (supplement) ◽

pp. S33

Author(s):

Koro Nishikata ◽

Mitsunori Ikeguchi ◽

Akinori Kidera

Keyword(s):

Molecular Dynamics ◽

Membrane Proteins ◽

Annual Meeting ◽

Biophysical Society ◽

New CHARMM force field parameters for dehydrated amino acid residues, the key to lantibiotic molecular dynamics simulations

RSC Advances ◽

10.1039/c4ra09897h ◽

2014 ◽

Vol 4 (89) ◽

pp. 48621-48631 ◽

Cited By ~ 9

Author(s):

Eleanor R. Turpin ◽

Sam Mulholland ◽

Andrew M. Teale ◽

Boyan B. Bonev ◽

Jonathan D. Hirst

Keyword(s):

Molecular Dynamics ◽

Amino Acid ◽

Force Field ◽

Amino Acid Residues ◽

Charmm Force Field ◽

Force Field Parameters ◽

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

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 ◽

Replica Exchange Molecular Dynamics ◽

Biophysical Society ◽

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

A test of improved force field parameters for urea: molecular-dynamics simulations of urea crystals

Journal of Molecular Modeling ◽

10.1007/s00894-011-1336-5 ◽

2012 ◽

Vol 18 (8) ◽

pp. 3455-3466 ◽

Cited By ~ 5

Author(s):

Gül Altınbaş Özpınar ◽

Frank R. Beierlein ◽

Wolfgang Peukert ◽

Dirk Zahn ◽

Timothy Clark

Keyword(s):

Molecular Dynamics ◽

Force Field ◽

Force Field Parameters ◽

2P135 Analysis of translocation of tRNA molecules through ribosome using electron microscopy density map and molecular dynamics simulations(The 48th Annual Meeting of the Biophysical Society of Japan)

Seibutsu Butsuri ◽

10.2142/biophys.50.s106_1 ◽

2010 ◽

Vol 50 (supplement2) ◽

pp. S106

Author(s):

Hisashi Ishida

Keyword(s):

Electron Microscopy ◽

Molecular Dynamics ◽

Annual Meeting ◽

Biophysical Society ◽

Density Map ◽