1P037 Integrated Hamiltonian Sampling: towards efficient free energy calculation and conformational sampling(01B. Protein : Structure & Function,Poster,The 52nd Annual Meeting of the Biophysical Society of Japan(BSJ2014))

Toshifumi Mori; Qiang Cui

doi:10.2142/biophys.54.s147_1

1P037 Integrated Hamiltonian Sampling: towards efficient free energy calculation and conformational sampling(01B. Protein : Structure & Function,Poster,The 52nd Annual Meeting of the Biophysical Society of Japan(BSJ2014))

Seibutsu Butsuri ◽

10.2142/biophys.54.s147_1 ◽

2014 ◽

Vol 54 (supplement1-2) ◽

pp. S147

Author(s):

Toshifumi Mori ◽

Qiang Cui

Keyword(s):

Free Energy ◽

Protein Structure ◽

Structure Function ◽

Annual Meeting ◽

Free Energy Calculation ◽

Conformational Sampling ◽

Energy Calculation ◽

Biophysical Society

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1P034 Conformational sampling of HP1 chromodomain/histone H3 tail complex(Protein: Structure & Function,Poster,The 52th Annual Meeting of the Biophysical Society of Japan(BSJ2014))

Seibutsu Butsuri ◽

10.2142/biophys.54.s146_4 ◽

2014 ◽

Vol 54 (supplement1-2) ◽

pp. S146

Author(s):

Hashiguchi Nobuto ◽

Omori Satoshi ◽

Moritsugu Kei ◽

Nishimura Yoshifumi ◽

Kidera Akinori

Keyword(s):

Protein Structure ◽

Structure Function ◽

Annual Meeting ◽

Histone H3 ◽

Conformational Sampling ◽

Biophysical Society ◽

Complex Protein

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2P021 Computational Drug Design by Accurate Free Energy Calculations(01B. Protein: Structure & Function,Poster,The 52nd Annual Meeting of the Biophysical Society of Japan(BSJ2014))

Seibutsu Butsuri ◽

10.2142/biophys.54.s198_3 ◽

2014 ◽

Vol 54 (supplement1-2) ◽

pp. S198

Author(s):

Hironori Kokubo ◽

Akihiro Yokota ◽

Nao Morishita ◽

Atsutoshi Okabe ◽

Etsurou Watanabe

Keyword(s):

Free Energy ◽

Protein Structure ◽

Drug Design ◽

Structure Function ◽

Annual Meeting ◽

Free Energy Calculations ◽

Computational Drug Design ◽

Energy Calculations ◽

Biophysical Society

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3P-134 Estimation of ligand binding free energies of F-ATPase by using molecular dynamics/free energy calculation(The 46th Annual Meeting of the Biophysical Society of Japan)

Seibutsu Butsuri ◽

10.2142/biophys.48.s148_3 ◽

2008 ◽

Vol 48 (supplement) ◽

pp. S148

Author(s):

Atsushi Suenaga ◽

Osamu Umezu ◽

Tadashi Ando ◽

Ichiro Yamato ◽

Takeshi Murata ◽

...

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Ligand Binding ◽

Annual Meeting ◽

Free Energy Calculation ◽

Energy Calculation ◽

Free Energies ◽

Biophysical Society ◽

Binding Free Energies

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1P021 Enhanced conformational sampling methods for extracting biological rare events of proteins(Protein: Structure & Function,Poster,The 52th Annual Meeting of the Biophysical Society of Japan(BSJ2014))

Seibutsu Butsuri ◽

10.2142/biophys.54.s144_3 ◽

2014 ◽

Vol 54 (supplement1-2) ◽

pp. S144

Author(s):

Harada Ryuhei ◽

Takano Yu ◽

Shigeta Yasuteru

Keyword(s):

Protein Structure ◽

Structure Function ◽

Annual Meeting ◽

Sampling Methods ◽

Rare Events ◽

Conformational Sampling ◽

Biophysical Society

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1PS020 Free energy calculation of lever-arm swing of myosin and the effect of actin filament(The 50th Annual Meeting of the Biophysical Society of Japan)

Seibutsu Butsuri ◽

10.2142/biophys.52.s77_3 ◽

2012 ◽

Vol 52 (supplement) ◽

pp. S77

Author(s):

Jun Ohnuki ◽

Takato Sato ◽

Koji Umezawa ◽

Mitsunori Takano

Keyword(s):

Free Energy ◽

Annual Meeting ◽

Actin Filament ◽

Free Energy Calculation ◽

Energy Calculation ◽

Arm Swing ◽

Lever Arm ◽

Biophysical Society

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3D1112 Reduction of side reaction due to mutations in P450 vitamin D3 hydroxylase : Free energy and quantum chemical calculations(3D Protein: Structure & Function 2,The 49th Annual Meeting of the Biophysical Society of Japan)

Seibutsu Butsuri ◽

10.2142/biophys.51.s118_4 ◽

2011 ◽

Vol 51 (supplement) ◽

pp. S118

Author(s):

Jiro Shimada ◽

Yoshifumi Fukunishi ◽

Hiroaki Fukunishi ◽

Hirotaka Yagi ◽

Hiroshi Isobe ◽

...

Keyword(s):

Free Energy ◽

Protein Structure ◽

Structure Function ◽

Annual Meeting ◽

Quantum Chemical Calculations ◽

Vitamin D3 ◽

Quantum Chemical ◽

Side Reaction ◽

3D Protein Structure ◽

Biophysical Society

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3P023 Predicting binding free energy of drug candidates to Factor Xa : 3D-RISM study(01B. Protein: Structure & Function,Poster,The 52nd Annual Meeting of the Biophysical Society of Japan(BSJ2014))

Seibutsu Butsuri ◽

10.2142/biophys.54.s252_5 ◽

2014 ◽

Vol 54 (supplement1-2) ◽

pp. S252

Author(s):

Sayaka Kohara ◽

Masatake Sugita ◽

Masanari Matsuoka ◽

Takeshi Kikuchi ◽

Fumio Hirata

Keyword(s):

Free Energy ◽

Protein Structure ◽

Structure Function ◽

Annual Meeting ◽

Binding Free Energy ◽

Factor Xa ◽

Drug Candidates ◽

Biophysical Society

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1P038 Full-scale conformational sampling of K63 and linear polyubiquitins(01B. Protein : Structure & Function,Poster,The 52nd Annual Meeting of the Biophysical Society of Japan(BSJ2014))

Seibutsu Butsuri ◽

10.2142/biophys.54.s147_2 ◽

2014 ◽

Vol 54 (supplement1-2) ◽

pp. S147

Author(s):

Masanori Shimizu ◽

Hafumi Nishi ◽

Kei Moritsugu ◽

Akinori Kidera

Keyword(s):

Protein Structure ◽

Structure Function ◽

Annual Meeting ◽

Full Scale ◽

Conformational Sampling ◽

Biophysical Society

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3P070 Multi-scale free energy calculation method with the combination of coarse-grained and all-atom models.(Protein: Property,The 48th Annual Meeting of the Biophysical Society of Japan)

Seibutsu Butsuri ◽

10.2142/biophys.50.s157_2 ◽

2010 ◽

Vol 50 (supplement2) ◽

pp. S157

Author(s):

Ryuhei Harada ◽

Akio Kitao

Keyword(s):

Free Energy ◽

Annual Meeting ◽

Calculation Method ◽

Coarse Grained ◽

Free Energy Calculation ◽

Energy Calculation ◽

Scale Free ◽

Multi Scale ◽

Protein Property ◽

Biophysical Society

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3P-011 Development of the free energy calculation method using a Brownian Dynamics/Umbrella Sampling(The 46th Annual Meeting of the Biophysical Society of Japan)

Seibutsu Butsuri ◽

10.2142/biophys.48.s129_4 ◽

2008 ◽

Vol 48 (supplement) ◽

pp. S129

Author(s):

Wankee Kim ◽

Tadashi Ando ◽

Ichiro Yamato

Keyword(s):

Free Energy ◽

Annual Meeting ◽

Calculation Method ◽

Brownian Dynamics ◽

Umbrella Sampling ◽

Free Energy Calculation ◽

Energy Calculation ◽

Biophysical Society

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