2SCP-05 Protein-ligand binding processes studied by coarse-grained molecular dynamics simulations(Prediction and analysis of protein functions from structural bioinformatics,Symposium,The 52th Annual Meeting of the Biophysical Society of Japan(BSJ2014))

Annual Meeting ◽

Structural Bioinformatics ◽

Coarse Grained ◽

Biophysical Society ◽

Protein Functions ◽

Dynamics Simulations ◽

1P-058 Molecular dynamics simulations of the ligand-binding core of inositol 1, 4, 5-trisphosphate receptor and its mutant in the ligand-free state(The 46th Annual Meeting of the Biophysical Society of Japan)

Seibutsu Butsuri ◽

10.2142/biophys.48.s30_1 ◽

2008 ◽

Vol 48 (supplement) ◽

pp. S30

Author(s):

Yoichi Ida ◽

Sotaro Fuchigamai ◽

Mitsunori Ikeguchi ◽

Akainori Kidera

Keyword(s):

Molecular Dynamics ◽

Ligand Binding ◽

Annual Meeting ◽

Inositol 1 ◽

Ligand Free ◽

Biophysical Society ◽

Binding Core ◽

Dynamics Simulations ◽

Trisphosphate Receptor

3C1024 Molecular dynamics simulations for glutamate-binding and cleft-closing processes of the ligand-binding domain of GluR2(3C Protein: Funcrion 2,The 49th Annual Meeting of the Biophysical Society of Japan)

Seibutsu Butsuri ◽

10.2142/biophys.51.s113_3 ◽

2011 ◽

Vol 51 (supplement) ◽

pp. S113

Author(s):

Okimasa Okada ◽

Kei Odai ◽

Tohru Sugimoto ◽

Etsuro Ito

Keyword(s):

Molecular Dynamics ◽

Ligand Binding ◽

Annual Meeting ◽

Binding Domain ◽

Ligand Binding Domain ◽

Glutamate Binding ◽

Biophysical Society ◽

Dynamics Simulations

Coarse-grained molecular dynamics simulations of protein-ligand binding

Journal of Computational Chemistry ◽

10.1002/jcc.23693 ◽

2014 ◽

Vol 35 (25) ◽

pp. 1835-1845 ◽

Cited By ~ 18

Author(s):

Tatsuki Negami ◽

Kentaro Shimizu ◽

Tohru Terada

Keyword(s):

Molecular Dynamics ◽

Ligand Binding ◽

Coarse Grained ◽

Dynamics Simulations ◽

1P058 Molecular dynamics simulations for structure changes of PRSet7 by ligand binding(01C. Protein : Property,Poster,The 52nd Annual Meeting of the Biophysical Society of Japan(BSJ2014))

Seibutsu Butsuri ◽

10.2142/biophys.54.s150_4 ◽

2014 ◽

Vol 54 (supplement1-2) ◽

pp. S150

Author(s):

Takako Sakano ◽

Hideaki Fujitani

Keyword(s):

Molecular Dynamics ◽

Ligand Binding ◽

Annual Meeting ◽

Structure Changes ◽

Protein Property ◽

Biophysical Society ◽

Dynamics Simulations

Understanding the mechanical and viscoelastic properties of graphene reinforced polycarbonate nanocomposites using coarse-grained molecular dynamics simulations

Computational Materials Science ◽

10.1016/j.commatsci.2021.110339 ◽

2021 ◽

Vol 191 ◽

pp. 110339

Author(s):

Jie Yang ◽

Daniel Custer ◽

Cho Chun Chiang ◽

Zhaoxu Meng ◽

X.H. Yao

Keyword(s):

Molecular Dynamics ◽

Viscoelastic Properties ◽

Coarse Grained ◽

Dynamics Simulations ◽

Effect of simulation temperature on phospholipid bilayer–vesicle transition studied by coarse-grained molecular dynamics simulations

Soft Matter ◽

10.1039/c3sm51038g ◽

2013 ◽

Vol 9 (30) ◽

pp. 7294 ◽

Cited By ~ 20

Author(s):

Choon-Peng Chng

Keyword(s):

Molecular Dynamics ◽

Phospholipid Bilayer ◽

Coarse Grained ◽

Dynamics Simulations ◽

Bilayer Vesicle ◽

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

Coarse-Grained Molecular Dynamics Simulations of Cobra Cytotoxin A3 Interactions with a Lipid Bilayer: Penetration of Loops into Membranes

The Journal of Physical Chemistry B ◽

10.1021/jp107599v ◽

2011 ◽

Vol 115 (5) ◽

pp. 796-802 ◽

Cited By ~ 11

Author(s):

Zhi-Yuan Su ◽

Yeng-Tseng Wang

Keyword(s):

Molecular Dynamics ◽

Lipid Bilayer ◽

Coarse Grained ◽

Dynamics Simulations ◽

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 ◽

Dynamics Simulations

Accurate Prediction of Forster Resonance Energy Transfer during Co-translational Folding with Coarse-Grained Molecular Dynamics Simulations

Biophysical Journal ◽

10.1016/j.bpj.2017.11.311 ◽

2018 ◽

Vol 114 (3) ◽

pp. 47a

Author(s):

Daniel A. Nissley ◽

Edward P. O'Brien

Keyword(s):

Molecular Dynamics ◽

Energy Transfer ◽

Resonance Energy Transfer ◽

Resonance Energy ◽

Accurate Prediction ◽

Coarse Grained ◽

Förster Resonance Energy Transfer ◽

Dynamics Simulations ◽