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Alchemical free energy calculations via metadynamics: Application to the theophylline‐RNA aptamer complex

Journal of computational chemistry, 2020-07, Vol.41 (20), p.1804-1819

2020

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Effect of N343 glycosylation and N501Y mutation on the SARS-CoV-2 spike protein: Modeling and MD Simulations

AIP Conference Proceedings, 2022, Vol.2611 (1)

2022

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High-Level ab Initio Calculations To Improve Protein Backbone Dihedral Parameters

Journal of chemical theory and computation, 2009-04, Vol.5 (4), p.1155-1165

2009

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Excited States of Phosphorescent Platinum(II) Complexes Containing N∧C∧N-Coordinating Tridentate Ligands: Spectroscopic Investigations and Time-Dependent Density Functional Theory Calculations

The journal of physical chemistry. A, Molecules, spectroscopy, kinetics, environment, & general theory, 2005-11, Vol.109 (43), p.9760-9766

2005

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Theoretical study on the absorption maxima of real GFPs

Chemical physics letters, 2010, Vol.484 (4), p.324-329

2010

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プローブ分子によるタンパク質の結合サイト探索

Journal of Computer Chemistry, Japan, 2017, Vol.16(4), pp.89-90

2017

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Accurate evaluation of the absorption maxima of retinal proteins based on a hybrid QM/MM method

Journal of computational chemistry, 2006-11, Vol.27 (14), p.1623-1630

2006

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Docking study and binding free energy calculation of poly (ADP-ribose) polymerase inhibitors

Journal of molecular modeling, 2011-02, Vol.17 (2), p.383-389

2011

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Binding pose prediction of a drug candidate, cepharanthine, targeting the SARS-Cov-2 spike protein using large-scale MD simulations

AIP Conference Proceedings, 2022, Vol.2611 (1)

2022

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Approach for Analyzing Protein Binding Sites Using Probe Molecules

Journal of Computer Chemistry, Japan, 2017, Vol.16(4), pp.89-90

2017

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Graph Classification of Molecules Using Force Field Atom and Bond Types

Molecular informatics, 2020-01, Vol.39 (1-2), p.e1800155-n/a

2020

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Analysis of the Hydration Site for Coagulation Factor Xa using Grid Inhomogeneous Solvation Theory

Journal of Computer Chemistry, Japan, 2016, Vol.15(3), pp.74-76

2016

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Prediction of the Multiple Binding Poses in Classical System Using Metadynamics

Journal of Computer Chemistry, Japan, 2016, Vol.15(3), pp.71-73

2016

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Binding Free Energy Calculation of Small Molecules to Rna with Multiple Binding Poses

Journal of Computer Chemistry, Japan, 2015, Vol.14(3), pp.80-82

2015

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Binding Free Energy Calculation of Small Molecules to Rna with Multiple Binding Poses

Journal of computer chemistry, Japan, 2015-01, Vol.14 (3), p.80-80

2015

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FMO Analysis for Intermoleular Interaction Energy between Human Coagulation Factor Xa and Four Ligands

Journal of Computer Chemistry, Japan, 2015, Vol.14(3), pp.54-56

2015

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Force Driving Cu Diffusion into Interlayer Dielectrics

Japanese Journal of Applied Physics, 2002-05, Vol.41 (Part 2, No. 5B), p.L537-L539

2002

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Quantum wire and dot formation by chemical vapor deposition and molecular layer deposition of one-dimensional conjugated polymer

Applied physics letters, 1992-01, Vol.60 (3), p.268-270

1992

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Binding Free Energy Calculations for Theophylline/Caffeine to RNA Aptamer

Journal of Computer Chemistry, Japan, 2014, Vol.13(3), pp.193-195

2014

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Massively parallel computation of absolute binding free energy with well-equilibrated states

Physical review. E, Statistical, nonlinear, and soft matter physics, 2009-02, Vol.79 (2 Pt 1), p.021914-021914, Article 021914

2009

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2P243 Quantum chemical study of the absorption maximum of channelrhodopsin(18A. Photobiology:Vision & Photoreception,Poster)

Seibutsu Butsuri, 2014/08/20, Vol.54(supplement1-2), pp.S235

2014

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2P243 チャネルロドプシンの吸収波長に関する量子化学的研究(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.S235

2014

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Docking study and binding free energy calculation of poly (ADP-ribose) polymerase inhibitors

Journal of molecular modeling, 2011-02, Vol.17 (2), p.383-389

2011

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Grid Inhomogeneous Solvation Theoryを用いた血液凝固因子Xaの水和サイト解析

Journal of Computer Chemistry, Japan, 2016, Vol.15(3), pp.74-76

2016

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古典ポテンシャル系のメタダイナミクスによる準安定構造探索

Journal of Computer Chemistry, Japan, 2016, Vol.15(3), pp.71-73

2016

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Alchemical free energy calculations via metadynamics: Application to the theophylline‐RNA aptamer complex

Effect of N343 glycosylation and N501Y mutation on the SARS-CoV-2 spike protein: Modeling and MD Simulations

High-Level ab Initio Calculations To Improve Protein Backbone Dihedral Parameters

Excited States of Phosphorescent Platinum(II) Complexes Containing N∧C∧N-Coordinating Tridentate Ligands: Spectroscopic Investigations and Time-Dependent Density Functional Theory Calculations

Theoretical study on the absorption maxima of real GFPs

プローブ分子によるタンパク質の結合サイト探索

Accurate evaluation of the absorption maxima of retinal proteins based on a hybrid QM/MM method

Docking study and binding free energy calculation of poly (ADP-ribose) polymerase inhibitors

Binding pose prediction of a drug candidate, cepharanthine, targeting the SARS-Cov-2 spike protein using large-scale MD simulations

Approach for Analyzing Protein Binding Sites Using Probe Molecules

Graph Classification of Molecules Using Force Field Atom and Bond Types

Analysis of the Hydration Site for Coagulation Factor Xa using Grid Inhomogeneous Solvation Theory

Prediction of the Multiple Binding Poses in Classical System Using Metadynamics

Binding Free Energy Calculation of Small Molecules to Rna with Multiple Binding Poses

Binding Free Energy Calculation of Small Molecules to Rna with Multiple Binding Poses

FMO Analysis for Intermoleular Interaction Energy between Human Coagulation Factor Xa and Four Ligands

Force Driving Cu Diffusion into Interlayer Dielectrics

Quantum wire and dot formation by chemical vapor deposition and molecular layer deposition of one-dimensional conjugated polymer

Binding Free Energy Calculations for Theophylline/Caffeine to RNA Aptamer

Massively parallel computation of absolute binding free energy with well-equilibrated states

2P243 Quantum chemical study of the absorption maximum of channelrhodopsin(18A. Photobiology:Vision & Photoreception,Poster)

2P243 チャネルロドプシンの吸収波長に関する量子化学的研究(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))

Docking study and binding free energy calculation of poly (ADP-ribose) polymerase inhibitors

Grid Inhomogeneous Solvation Theoryを用いた血液凝固因子Xaの水和サイト解析

古典ポテンシャル系のメタダイナミクスによる準安定構造探索

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