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Flexible selection of the solute region in replica exchange with solute tempering: Application to protein-folding simulations

The Journal of chemical physics, 2018-08, Vol.149 (7), p.072304-072304

2018

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Encounter complexes and hidden poses of kinase-inhibitor binding on the free-energy landscape

Proceedings of the National Academy of Sciences - PNAS, 2019-09, Vol.116 (37), p.18404-18409

2019

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Facile Catch and Release of Fullerenes Using a Photoresponsive Molecular Tube

Journal of the American Chemical Society, 2013-09, Vol.135 (35), p.12976-12979

2013

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De Novo Prediction of Binders and Nonbinders for T4 Lysozyme by gREST Simulations

Journal of chemical information and modeling, 2019-09, Vol.59 (9), p.3879-3888

2019

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Photoactivation Intermediates of a G‑Protein Coupled Receptor Rhodopsin Investigated by a Hybrid Molecular Simulation

The journal of physical chemistry. B, 2017-04, Vol.121 (15), p.3842-3852

2017

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Role of the N‐Terminal Transmembrane Helix Contacts in the Activation of FGFR3

Journal of computational chemistry, 2020-03, Vol.41 (6), p.561-572

2020

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Molecular Mechanism of Wide Photoabsorption Spectral Shifts of Color Variants of Human Cellular Retinol Binding Protein II

Journal of the American Chemical Society, 2015-10, Vol.137 (41), p.13362-13370

2015

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Use of multistate Bennett acceptance ratio method for free-energy calculations from enhanced sampling and free-energy perturbation

Biophysical reviews, 2022-12, Vol.14 (6), p.1503-1512

2022

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An Atomistic Model of a Precursor State of Light-Induced Channel Opening of Channelrhodopsin

Biophysical journal, 2018-10, Vol.115 (7), p.1281-1291

2018

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QM/MM Geometry Optimization on Extensive Free-Energy Surfaces for Examination of Enzymatic Reactions and Design of Novel Functional Properties of Proteins

Annual review of physical chemistry, 2017-05, Vol.68 (1), p.135-154

2017

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Molecular Mechanism of ATP Hydrolysis in F1-ATPase Revealed by Molecular Simulations and Single-Molecule Observations

Journal of the American Chemical Society, 2012-05, Vol.134 (20), p.8447-8454

2012

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A Blue-shifted Light-driven Proton Pump for Neural Silencing

The Journal of biological chemistry, 2013-07, Vol.288 (28), p.20624-20632

2013

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Molecular Dynamics of Channelrhodopsin at the Early Stages of Channel Opening

PloS one, 2015-06, Vol.10 (6), p.e0131094-e0131094

2015

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Structural and spectral characterizations of C1C2 channelrhodopsin and its mutants by molecular simulations

Chemical physics letters, 2013-01, Vol.556, p.266-271

2013

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A Molecular Dynamics Study for the Structure Determination of the Signaling State in the Photocycle of Photoactive Yellow Protein

The journal of physical chemistry. B, 2010-05, Vol.114 (19), p.6594-6600

2010

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Flexible Choice of Solute in Replica Exchange with Solute Tempering Can Improve Performance of Conformation Search for Small Proteins

Biophysical journal, 2018-02, Vol.114 (3), p.676a-676a

2018

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GENESIS 1.1: A hybrid‐parallel molecular dynamics simulator with enhanced sampling algorithms on multiple computational platforms

Journal of computational chemistry, 2017-09, Vol.38 (25), p.2193-2206

2017

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Proton Transfer and Associated Molecular Rearrangements in the Photocycle of Photoactive Yellow Protein: Role of Water Molecular Migration on the Proton Transfer Reaction

The journal of physical chemistry. B, 2007-03, Vol.111 (11), p.2948-2956

2007

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Replica-Exchange Methods for Biomolecular Simulations

Methods in molecular biology (Clifton, N.J.), 2019, Vol.2022, p.155

2019

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Molecular Mechanism of ATP Hydrolysis in F 1 -ATPase Revealed by Molecular Simulations and Single-Molecule Observations

Journal of the American Chemical Society, 2012-05, Vol.134 (20), p.8447-8454

2012

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Atomistic design of microbial opsin-based blue-shifted optogenetics tools

Nature communications, 2015-05, Vol.6 (1), p.7177-7177, Article 7177

2015

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1P245 A theoretical study on early intermediates of bovine rhodopsin by QM/MM RWFE method(18A. Photobiology:Vision & Photoreception,Poster,The 52nd Annual Meeting of the Biophysical Society of Japan(BSJ2014))

Seibutsu Butsuri, 2014/08/20, Vol.54(supplement1-2), pp.S181

2014

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1P245 QM/MM RWFE法によるウシロドプシンの光反応中間体に関する理論研究(18A. 光生物:視覚・光受容,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.S181

2014

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3P244 QM/MM RWFE法によるロドプシンの光反応中間体に関する理論研究(18A.光生物:視覚・光受容,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.S252

2013

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3P244 A theoretical study on early intermediates of bovine rhodopsin by QM/MM RWFE method(18A. Photobiology: Vision & Photoreception,Poster)

Seibutsu Butsuri, 2013/09/13, Vol.53(supplement1-2), pp.S252

2013

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Flexible selection of the solute region in replica exchange with solute tempering: Application to protein-folding simulations

Encounter complexes and hidden poses of kinase-inhibitor binding on the free-energy landscape

Facile Catch and Release of Fullerenes Using a Photoresponsive Molecular Tube

De Novo Prediction of Binders and Nonbinders for T4 Lysozyme by gREST Simulations

Photoactivation Intermediates of a G‑Protein Coupled Receptor Rhodopsin Investigated by a Hybrid Molecular Simulation

Role of the N‐Terminal Transmembrane Helix Contacts in the Activation of FGFR3

Molecular Mechanism of Wide Photoabsorption Spectral Shifts of Color Variants of Human Cellular Retinol Binding Protein II

Use of multistate Bennett acceptance ratio method for free-energy calculations from enhanced sampling and free-energy perturbation

An Atomistic Model of a Precursor State of Light-Induced Channel Opening of Channelrhodopsin

QM/MM Geometry Optimization on Extensive Free-Energy Surfaces for Examination of Enzymatic Reactions and Design of Novel Functional Properties of Proteins

Molecular Mechanism of ATP Hydrolysis in F1-ATPase Revealed by Molecular Simulations and Single-Molecule Observations

A Blue-shifted Light-driven Proton Pump for Neural Silencing

Molecular Dynamics of Channelrhodopsin at the Early Stages of Channel Opening

Structural and spectral characterizations of C1C2 channelrhodopsin and its mutants by molecular simulations

A Molecular Dynamics Study for the Structure Determination of the Signaling State in the Photocycle of Photoactive Yellow Protein

Flexible Choice of Solute in Replica Exchange with Solute Tempering Can Improve Performance of Conformation Search for Small Proteins

GENESIS 1.1: A hybrid‐parallel molecular dynamics simulator with enhanced sampling algorithms on multiple computational platforms

Proton Transfer and Associated Molecular Rearrangements in the Photocycle of Photoactive Yellow Protein: Role of Water Molecular Migration on the Proton Transfer Reaction

Replica-Exchange Methods for Biomolecular Simulations

Molecular Mechanism of ATP Hydrolysis in F 1 -ATPase Revealed by Molecular Simulations and Single-Molecule Observations

Atomistic design of microbial opsin-based blue-shifted optogenetics tools

1P245 A theoretical study on early intermediates of bovine rhodopsin by QM/MM RWFE method(18A. Photobiology:Vision & Photoreception,Poster,The 52nd Annual Meeting of the Biophysical Society of Japan(BSJ2014))

1P245 QM/MM RWFE法によるウシロドプシンの光反応中間体に関する理論研究(18A. 光生物:視覚・光受容,ポスター,第52回日本生物物理学会年会(2014年度))

3P244 QM/MM RWFE法によるロドプシンの光反応中間体に関する理論研究(18A.光生物:視覚・光受容,ポスター,日本生物物理学会年会第51回(2013年度))

3P244 A theoretical study on early intermediates of bovine rhodopsin by QM/MM RWFE method(18A. Photobiology: Vision & Photoreception,Poster)

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