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Modeling Structural Dynamics of Biomolecular Complexes by Coarse-Grained Molecular Simulations

Accounts of chemical research, 2015-12, Vol.48 (12), p.3026-3035

2015

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Partial Unwrapping and Histone Tail Dynamics in Nucleosome Revealed by Coarse-Grained Molecular Simulations

PLoS computational biology, 2015-08, Vol.11 (8), p.e1004443-e1004443

2015

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Nucleosome Crowding in Chromatin Slows the Diffusion but Can Promote Target Search of Proteins

Biophysical journal, 2019-06, Vol.116 (12), p.2285-2295

2019

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p53 Searches on DNA by Rotation-Uncoupled Sliding at C‑Terminal Tails and Restricted Hopping of Core Domains

Journal of the American Chemical Society, 2012-09, Vol.134 (35), p.14555-14562

2012

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CafeMol: A Coarse-Grained Biomolecular Simulator for Simulating Proteins at Work

Journal of chemical theory and computation, 2011-06, Vol.7 (6), p.1979-1989

2011

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Drug export and allosteric coupling in a multidrug transporter revealed by molecular simulations

Nature communications, 2010-11, Vol.1 (8), p.117-117, Article 117

2010

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Structure-based molecular simulations reveal the enhancement of biased Brownian motions in single-headed kinesin

PLoS computational biology, 2013-02, Vol.9 (2), p.e1002907-e1002907

2013

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Partial Unwrapping and Histone Tail Dynamics in Nucleosome Revealed by Coarse-Grained Molecular Simulations: e1004443

PLoS computational biology, 2015-08, Vol.11 (8)

2015

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2P119 Functionally rotating mechanism of a multidrug transporter studied by coarse-grained simulation(The 48th Annual Meeting of the Biophysical Society of Japan)

Seibutsu Butsuri, 2010/08/15, Vol.50(supplement2), pp.S103

2010

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Free-energy landscape of kinesin by a realistic lattice model

Proteins, structure, function, and bioinformatics, 2008-04, Vol.71 (1), p.389-395

2008

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2P124 Structural sampling of polynucleosome by coarse-grained simulations(05B. Nucleic acid: Interaction & Complex formation,Poster,The 52nd Annual Meeting of the Biophysical Society of Japan(BSJ2014))

Seibutsu Butsuri, 2014/08/20, Vol.54(supplement1-2), pp.S215

2014

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2P124 粗視化シミュレーションによる多ヌクレオソーム系の構造サンプリング(05B. 核酸:相互作用・複合体,ポスター,第52回日本生物物理学会年会(2014年度))

生物物理, 2014/08/20, Vol.54(supplement1-2), pp.S215

2014

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3TA3-02 Functionally rotating mechanism of a multidrug transporter studied by coarse-grained simulation(The 47th Annual Meeting of the Biophysical Society of Japan)

Seibutsu Butsuri, 2009/09/20, Vol.49(supplement), pp.S54-S55

2009

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3P-182 Functionally rotating mechanism of a multidrug transporter studied by coarse-grained simulation(Biol & Artifi memb.:Dynamics,Oral Presentations,The 47th Annual Meeting of the Biophysical Society of Japan)

Seibutsu Butsuri, 2009/09/20, Vol.49(supplement), pp.S182

2009

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3P121 粗視化シミュレーションによる多ヌクレオソーム系の構造ダイナミクス(05A.核酸:構造・物性,ポスター,日本生物物理学会年会第51回(2013年度))

生物物理, 2013/09/13, Vol.53(supplement1-2), pp.S231

2013

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3P121 Poly-nucleosome structural dynamics by coarse-grained simulations(05A. Nucleic acid: Structure & Property,Poster)

Seibutsu Butsuri, 2013/09/13, Vol.53(supplement1-2), pp.S231

2013

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1P588 Conformational change of proteins described by extended Go-like models(27. Molecular dynamics simulation,Poster Session,Abstract,Meeting Program of EABS & BSJ 2006)

Seibutsu Butsuri, 2006/10/01, Vol.46(supplement2), pp.S293

2006

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Diversity in free energy landscape and folding pathway of proteins with the same native topology

Chemical physics letters, 2006-08, Vol.427 (4), p.414-417

2006

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Functionally Rotating Mechanism of a Multidrug Transporter Studied by Coarse-Grained Simulation

Biophysical journal, 2010-01, Vol.98 (3), p.685a-685a

2010

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3PT009 粗視化シミュレーションによる単/多ヌクレオソーム系の構造ダイナミクス(日本生物物理学会第50回年会(2012年度))

生物物理, 2012/08/15, Vol.52(supplement), pp.S156-S157

2012

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3PT009 Mono- and poly-nucleosome structural dynamics by coarse-grained simulations(The 50th Annual Meeting of the Biophysical Society of Japan)

Seibutsu Butsuri, 2012/08/15, Vol.52(supplement), pp.S156-S157

2012

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1C1436 粗視化モデルによる複数のヌクレオソームのシミュレーション(核酸,第49回日本生物物理学会年会)

生物物理, 2011/08/15, Vol.51(supplement), pp.S34-S35

2011

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1C1436 Coarse-grained simulations of multi-nucleosome systems(Nucleic acid,The 49th Annual Meeting of the Biophysical Society of Japan)

Seibutsu Butsuri, 2011/08/15, Vol.51(supplement), pp.S34-S35

2011

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Mechanism of Unidirectional Move of KIF1A Motor Studied by Coarse-Grained Simulations

Biophysical journal, 2010-01, Vol.98 (3), p.167a-167a

2010

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1P136 Coarse-grained simulation of protein-DNA complex : mechanical unzipping of nucleosome(Nucleic acid:Interaction & Complex formation,The 48th Annual Meeting of the Biophysical Society of Japan)

Seibutsu Butsuri, 2010/08/15, Vol.50(supplement2), pp.S43

2010

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Modeling Structural Dynamics of Biomolecular Complexes by Coarse-Grained Molecular Simulations

Partial Unwrapping and Histone Tail Dynamics in Nucleosome Revealed by Coarse-Grained Molecular Simulations

Nucleosome Crowding in Chromatin Slows the Diffusion but Can Promote Target Search of Proteins

p53 Searches on DNA by Rotation-Uncoupled Sliding at C‑Terminal Tails and Restricted Hopping of Core Domains

CafeMol: A Coarse-Grained Biomolecular Simulator for Simulating Proteins at Work

Drug export and allosteric coupling in a multidrug transporter revealed by molecular simulations

Structure-based molecular simulations reveal the enhancement of biased Brownian motions in single-headed kinesin

Partial Unwrapping and Histone Tail Dynamics in Nucleosome Revealed by Coarse-Grained Molecular Simulations: e1004443

2P119 Functionally rotating mechanism of a multidrug transporter studied by coarse-grained simulation(The 48th Annual Meeting of the Biophysical Society of Japan)

Free-energy landscape of kinesin by a realistic lattice model

2P124 Structural sampling of polynucleosome by coarse-grained simulations(05B. Nucleic acid: Interaction & Complex formation,Poster,The 52nd Annual Meeting of the Biophysical Society of Japan(BSJ2014))

2P124 粗視化シミュレーションによる多ヌクレオソーム系の構造サンプリング(05B. 核酸:相互作用・複合体,ポスター,第52回日本生物物理学会年会(2014年度))

3TA3-02 Functionally rotating mechanism of a multidrug transporter studied by coarse-grained simulation(The 47th Annual Meeting of the Biophysical Society of Japan)

3P-182 Functionally rotating mechanism of a multidrug transporter studied by coarse-grained simulation(Biol & Artifi memb.:Dynamics,Oral Presentations,The 47th Annual Meeting of the Biophysical Society of Japan)

3P121 粗視化シミュレーションによる多ヌクレオソーム系の構造ダイナミクス(05A.核酸:構造・物性,ポスター,日本生物物理学会年会第51回(2013年度))

3P121 Poly-nucleosome structural dynamics by coarse-grained simulations(05A. Nucleic acid: Structure & Property,Poster)

1P588 Conformational change of proteins described by extended Go-like models(27. Molecular dynamics simulation,Poster Session,Abstract,Meeting Program of EABS & BSJ 2006)

Diversity in free energy landscape and folding pathway of proteins with the same native topology

Functionally Rotating Mechanism of a Multidrug Transporter Studied by Coarse-Grained Simulation

3PT009 粗視化シミュレーションによる単/多ヌクレオソーム系の構造ダイナミクス(日本生物物理学会第50回年会(2012年度))

3PT009 Mono- and poly-nucleosome structural dynamics by coarse-grained simulations(The 50th Annual Meeting of the Biophysical Society of Japan)

1C1436 粗視化モデルによる複数のヌクレオソームのシミュレーション(核酸,第49回日本生物物理学会年会)

1C1436 Coarse-grained simulations of multi-nucleosome systems(Nucleic acid,The 49th Annual Meeting of the Biophysical Society of Japan)

Mechanism of Unidirectional Move of KIF1A Motor Studied by Coarse-Grained Simulations

1P136 Coarse-grained simulation of protein-DNA complex : mechanical unzipping of nucleosome(Nucleic acid:Interaction & Complex formation,The 48th Annual Meeting of the Biophysical Society of Japan)

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