3G1148 P15 Solvation Free Energy of Complex : a potential tool for improving scoring function in protein-protein docking(3G Protein: Structure 3,The 49th Annual Meeting of the Biophysical Society of Japan)

Kazuhiro Takemura; Hao Guo; Shun Sakuraba; Nobuyuki Matubayashi; Akio Kitao

doi:10.2142/biophys.51.s130_4

3G1148 P15 Solvation Free Energy of Complex : a potential tool for improving scoring function in protein-protein docking(3G Protein: Structure 3,The 49th Annual Meeting of the Biophysical Society of Japan)

Seibutsu Butsuri ◽

10.2142/biophys.51.s130_4 ◽

2011 ◽

Vol 51 (supplement) ◽

pp. S130

Author(s):

Kazuhiro Takemura ◽

Hao Guo ◽

Shun Sakuraba ◽

Nobuyuki Matubayashi ◽

Akio Kitao

Keyword(s):

Free Energy ◽

Protein Structure ◽

Annual Meeting ◽

Scoring Function ◽

Solvation Free Energy ◽

Protein Docking ◽

Biophysical Society ◽

Potential Tool

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3P-038 Solvation free energy of globular protein: an estimation by means of energy representation method(Protein:Property,The 47th Annual Meeting of the Biophysical Society of Japan)

Seibutsu Butsuri ◽

10.2142/biophys.49.s157_3 ◽

2009 ◽

Vol 49 (supplement) ◽

pp. S157

Author(s):

Hiroaki Saito ◽

Keisuke Matsumoto ◽

Riki Nakamura ◽

Taku Mizukami ◽

Kiyoshi Nishikawa ◽

...

Keyword(s):

Free Energy ◽

Annual Meeting ◽

Solvation Free Energy ◽

Globular Protein ◽

Biophysical Society ◽

Representation Method

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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 ◽

Replica Exchange Molecular Dynamics ◽

Protein Property ◽

Biophysical Society

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1P129 Free-energy analysis of the effect of ions on protein structure(07. Water & Hydration & Electrolyte,Poster,The 52nd Annual Meeting of the Biophysical Society of Japan(BSJ2014))

Seibutsu Butsuri ◽

10.2142/biophys.54.s162_3 ◽

2014 ◽

Vol 54 (supplement1-2) ◽

pp. S162

Author(s):

Yasuhito Karino ◽

Yuji Sugita

Keyword(s):

Free Energy ◽

Protein Structure ◽

Annual Meeting ◽

Energy Analysis ◽

Biophysical Society ◽

Free Energy Analysis

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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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3P016 Introducing intramolecular flexibility into protein-protein docking(Protein: Structure,The 48th Annual Meeting of the Biophysical Society of Japan)

Seibutsu Butsuri ◽

10.2142/biophys.50.s147_4 ◽

2010 ◽

Vol 50 (supplement2) ◽

pp. S147

Author(s):

Kazuya Sumikoshi ◽

Shugo Nakamura ◽

Kentaro Shimizu

Keyword(s):

Protein Structure ◽

Annual Meeting ◽

Protein Docking ◽

Biophysical Society ◽

Docking Protein

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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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1PT001 Solvation free energy in protein dochking process(The 50th Annual Meeting of the Biophysical Society of Japan)

Seibutsu Butsuri ◽

10.2142/biophys.52.s83_3 ◽

2012 ◽

Vol 52 (supplement) ◽

pp. S83

Author(s):

Taku Mizukami ◽

Hiroaki Siato ◽

Hidemi Nagao

Keyword(s):

Free Energy ◽

Annual Meeting ◽

Solvation Free Energy ◽

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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2P-071 Molecular and thermodynamic basis of osmolyte effects to proteins by solvation free energy calculations(The 46th Annual Meeting of the Biophysical Society of Japan)

Seibutsu Butsuri ◽

10.2142/biophys.48.s86_1 ◽

2008 ◽

Vol 48 (supplement) ◽

pp. S86

Author(s):

Hironori Kokubo ◽

B.M. Pettitt

Keyword(s):

Free Energy ◽

Annual Meeting ◽

Solvation Free Energy ◽

Free Energy Calculations ◽

Energy Calculations ◽

Biophysical Society ◽

Thermodynamic Basis

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1P059 Fluctuation of solvation free energy of globular protein by all-atom molecular dynamics simulation(Protein:Property,The 48th Annual Meeting of the Biophysical Society of Japan)

Seibutsu Butsuri ◽

10.2142/biophys.50.s29_4 ◽

2010 ◽

Vol 50 (supplement2) ◽

pp. S29

Author(s):

Hiroaki Saito ◽

Kiyoshi Nishikawa ◽

Hidemi Nagao

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulation ◽

Annual Meeting ◽

Solvation Free Energy ◽

Globular Protein ◽

Dynamics Simulation ◽

Biophysical Society

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