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A cutoff-based method with charge-distribution-data driven pair potentials for efficiently estimating electrostatic interactions in molecular systems

The Journal of chemical physics, 2023-12, Vol.159 (23)

2023

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Multiple protonation states in ligand-free SARS-CoV-2 main protease revealed by large-scale quantum molecular dynamics simulations

Chemical physics letters, 2022-05, Vol.794, p.139489-139489, Article 139489

2022

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Generalized–ensemble method study: A helix‐mimetic compound inhibits protein–protein interaction by long‐range and short‐range intermolecular interactions

Journal of computational chemistry, 2021-05, Vol.42 (14), p.956-969

2021

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Prediction of Synthetic Accessibility Based on Commercially Available Compound Databases

Journal of chemical information and modeling, 2014-12, Vol.54 (12), p.3259-3267

2014

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Computer simulation of molecular recognition in biomolecular system: from in silico screening to generalized ensembles

Biophysical reviews, 2022-12, Vol.14 (6), p.1423-1447

2022

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Cryptic-site binding mechanism of medium-sized Bcl-xL inhibiting compounds elucidated by McMD-based dynamic docking simulations

Scientific reports, 2021-03, Vol.11 (1), p.5046-5046, Article 5046

2021

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Difference of binding modes among three ligands to a receptor mSin3B corresponding to their inhibitory activities

Scientific reports, 2021-03, Vol.11 (1), p.6178-6178, Article 6178

2021

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Structural Fluctuations of Aromatic Residues in an Apo-Form Reveal Cryptic Binding Sites: Implications for Fragment-Based Drug Design

The journal of physical chemistry. B, 2020-11, Vol.124 (45), p.9977-9986

2020

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Structure-based drug screening and ligand-based drug screening with machine learning

Combinatorial chemistry & high throughput screening, 2009-05, Vol.12 (4), p.397

Fukunishi, Yoshifumi

2009

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Prediction of ligand‐binding sites of proteins by molecular docking calculation for a random ligand library

Protein science, 2011-01, Vol.20 (1), p.95-106

2011

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Flexibility and Cell Permeability of Cyclic Ras-Inhibitor Peptides Revealed by the Coupled Nosé–Hoover Equation

Journal of chemical information and modeling, 2021-04, Vol.61 (4), p.1921-1930

2021

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A2B adenosine receptor inhibition by the dihydropyridine calcium channel blocker nifedipine involves colonic fluid secretion

Scientific reports, 2020-02, Vol.10 (1), p.3555-3555, Article 3555

2020

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Prediction of Protein−compound Binding Energies from Known Activity Data: Docking‐score‐based Method and its Applications

Molecular informatics, 2018-07, Vol.37 (6-7), p.e1700120-n/a

2018

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Post processing of protein-compound docking for fragment-based drug discovery (FBDD): in-silico structure-based drug screening and ligand-binding pose prediction

Current topics in medicinal chemistry, 2010-04, Vol.10 (6), p.680

Fukunishi, Yoshifumi

2010

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Asymmetric dynamics of dimeric SARS-CoV-2 and SARS-CoV main proteases in an apo form: Molecular dynamics study on fluctuations of active site, catalytic dyad, and hydration water

BBA advances, 2021, Vol.1, p.100016-100016, Article 100016

2021

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Fly casting with ligand sliding and orientational selection supporting complex formation of a GPCR and a middle sized flexible molecule

Scientific reports, 2022-08, Vol.12 (1), p.13792-13792, Article 13792

2022

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Free-energy landscape of molecular interactions between endothelin 1 and human endothelin type B receptor: fly-casting mechanism

Protein engineering, design and selection, 2019-12, Vol.32 (7), p.297-308

2019

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Virtual-system-coupled adaptive umbrella sampling to compute free-energy landscape for flexible molecular docking

Journal of computational chemistry, 2015-07, Vol.36 (20), p.1489-1501

2015

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Investigation on substrate specificity and catalytic activity of serine protease neuropsin

Biophysics and Physicobiology, 2022, Vol.19, pp.e190040

2022

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Binding free-energy landscapes of small molecule binder and non-binder to FMN riboswitch: All-atom molecular dynamics

Biophysics and Physicobiology, 2023, Vol.20(4), pp.e200047

2023

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Binding Mechanism of Riboswitch to Natural Ligand Elucidated by McMD-Based Dynamic Docking Simulations

ACS omega, 2024-01, Vol.9 (3), p.3412-3422

2024

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GA-guided mD-VcMD: A genetic-algorithm-guided method for multi-dimensional virtual-system coupled molecular dynamics

Biophysics and Physicobiology, 2020, Vol.17, pp.161-176

2020

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Computational Study of Drug Binding Affinity to Influenza A Neuraminidase Using Smooth Reaction Path Generation (SRPG) Method

Journal of chemical information and modeling, 2015-09, Vol.55 (9), p.1936-1943

2015

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The Filling Potential Method: A Method for Estimating the Free Energy Surface for Protein−Ligand Docking

The journal of physical chemistry. B, 2003-11, Vol.107 (47), p.13201-13210

2003

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Quantitative Structure‐activity Relationship (QSAR) Models for Docking Score Correction

Molecular informatics, 2017-01, Vol.36 (1-2), p.n/a

2017

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A cutoff-based method with charge-distribution-data driven pair potentials for efficiently estimating electrostatic interactions in molecular systems

Multiple protonation states in ligand-free SARS-CoV-2 main protease revealed by large-scale quantum molecular dynamics simulations

Generalized–ensemble method study: A helix‐mimetic compound inhibits protein–protein interaction by long‐range and short‐range intermolecular interactions

Prediction of Synthetic Accessibility Based on Commercially Available Compound Databases

Computer simulation of molecular recognition in biomolecular system: from in silico screening to generalized ensembles

Cryptic-site binding mechanism of medium-sized Bcl-xL inhibiting compounds elucidated by McMD-based dynamic docking simulations

Difference of binding modes among three ligands to a receptor mSin3B corresponding to their inhibitory activities

Structural Fluctuations of Aromatic Residues in an Apo-Form Reveal Cryptic Binding Sites: Implications for Fragment-Based Drug Design

Structure-based drug screening and ligand-based drug screening with machine learning

Prediction of ligand‐binding sites of proteins by molecular docking calculation for a random ligand library

Flexibility and Cell Permeability of Cyclic Ras-Inhibitor Peptides Revealed by the Coupled Nosé–Hoover Equation

A2B adenosine receptor inhibition by the dihydropyridine calcium channel blocker nifedipine involves colonic fluid secretion

Prediction of Protein−compound Binding Energies from Known Activity Data: Docking‐score‐based Method and its Applications

Post processing of protein-compound docking for fragment-based drug discovery (FBDD): in-silico structure-based drug screening and ligand-binding pose prediction

Asymmetric dynamics of dimeric SARS-CoV-2 and SARS-CoV main proteases in an apo form: Molecular dynamics study on fluctuations of active site, catalytic dyad, and hydration water

Fly casting with ligand sliding and orientational selection supporting complex formation of a GPCR and a middle sized flexible molecule

Free-energy landscape of molecular interactions between endothelin 1 and human endothelin type B receptor: fly-casting mechanism

Virtual-system-coupled adaptive umbrella sampling to compute free-energy landscape for flexible molecular docking

Investigation on substrate specificity and catalytic activity of serine protease neuropsin

Binding free-energy landscapes of small molecule binder and non-binder to FMN riboswitch: All-atom molecular dynamics

Binding Mechanism of Riboswitch to Natural Ligand Elucidated by McMD-Based Dynamic Docking Simulations

GA-guided mD-VcMD: A genetic-algorithm-guided method for multi-dimensional virtual-system coupled molecular dynamics

Computational Study of Drug Binding Affinity to Influenza A Neuraminidase Using Smooth Reaction Path Generation (SRPG) Method

The Filling Potential Method: A Method for Estimating the Free Energy Surface for Protein−Ligand Docking

Quantitative Structure‐activity Relationship (QSAR) Models for Docking Score Correction

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