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3D-RISM-AI: A Machine Learning Approach to Predict Protein–Ligand Binding Affinity Using 3D-RISM

The journal of physical chemistry. B, 2022-08, Vol.126 (33), p.6148-6158

2022

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Allosteric Regulation of 3CL Protease of SARS-CoV-2 and SARS-CoV Observed in the Crystal Structure Ensemble

Journal of molecular biology, 2021-12, Vol.433 (24), p.167324-167324, Article 167324

2021

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Binding and Unbinding Pathways of Peptide Substrates on the SARS-CoV‑2 3CL Protease

Journal of chemical information and modeling, 2023-01, Vol.63 (1), p.240-250

2023

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Structure of SARS-CoV-2 membrane protein essential for virus assembly

Nature communications, 2022-08, Vol.13 (1), p.4399-4399, Article 4399

2022

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Mechanism of Vitamin D Receptor Ligand-Binding Domain Regulation Studied by gREST Simulations

Journal of chemical information and modeling, 2021-07, Vol.61 (7), p.3625-3637

2021

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An accurate and rapid method for calculating hydration free energies of a variety of solutes including proteins

The Journal of chemical physics, 2019-05, Vol.150 (17), p.175101-175101

2019

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Effect of Water Molecules on the Activating S810L Mutation of the Mineralocorticoid Receptor

Journal of chemical information and modeling, 2021-07, Vol.61 (7), p.3583-3592

2021

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A synthetic ion channel with anisotropic ligand response

Nature communications, 2020-06, Vol.11 (1), p.2924-2924, Article 2924

2020

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Elimination of Finite-Size Effects on Binding Free Energies via the Warp-Drive Method

Journal of chemical theory and computation, 2018-12, Vol.14 (12), p.6544-6559

2018

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TLR3 forms a laterally aligned multimeric complex along double-stranded RNA for efficient signal transduction

Nature communications, 2023-01, Vol.14 (1), p.164-164, Article 164

2023

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Supramolecular Mechanosensitive Potassium Channel Formed by Fluorinated Amphiphilic Cyclophane

Journal of the American Chemical Society, 2022-07, Vol.144 (26), p.11802-11809

2022

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Development of the force field for cyclosporine A

Biophysics and Physicobiology, 2022, Vol.19, pp.e190045

2022

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Functional dynamics of SARS-CoV-2 3C-like protease as a member of clan PA

Biophysical reviews, 2022-12, Vol.14 (6), p.1473-1485

2022

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Serine 298 Phosphorylation in Linker 2 of UHRF1 Regulates Ligand-Binding Property of Its Tandem Tudor Domain

Journal of molecular biology, 2020-06, Vol.432 (14), p.4061-4075

2020

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Mandibulofacial dysostosis with alopecia results from ETAR gain-of-function mutations via allosteric effects on ligand binding

The Journal of clinical investigation, 2023-02, Vol.133 (4), p.1-13

2023

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Structural basis for ligand recognition and signaling of hydroxy-carboxylic acid receptor 2

Nature communications, 2023-11, Vol.14 (1), p.7150-7150, Article 7150

2023

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Imidazolinium‐based Multiblock Amphiphile as Transmembrane Anion Transporter

Chemistry, an Asian journal, 2021-01, Vol.16 (2), p.147-157

2021

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Comparison of the Molecular Motility of Tubulin Dimeric Isoforms: Molecular Dynamics Simulations and Diffracted X-ray Tracking Study

International journal of molecular sciences, 2023-10, Vol.24 (20), p.15423

2023

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Apo- and Antagonist-Binding Structures of Vitamin D Receptor Ligand-Binding Domain Revealed by Hybrid Approach Combining Small-Angle X‑ray Scattering and Molecular Dynamics

Journal of medicinal chemistry, 2016-09, Vol.59 (17), p.7888-7900

2016

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Rotation Mechanism of Molecular Motor V1-ATPase Studied by Multiscale Molecular Dynamics Simulation

Biophysical journal, 2017-03, Vol.112 (5), p.911-920

2017

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Finite-Size Effect on the Charging Free Energy of Protein in Explicit Solvent

Journal of chemical theory and computation, 2015-01, Vol.11 (1), p.215-223

2015

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An accurate and efficient computation method of the hydration free energy of a large, complex molecule

The Journal of chemical physics, 2015-05, Vol.142 (17), p.175101-175101

2015

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Rotational Mechanism Model of the Bacterial V1 Motor Based on Structural and Computational Analyses

Frontiers in physiology, 2019-02, Vol.10, p.46-46

2019

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Combination of coarse-grained molecular dynamics simulations and small-angle X-ray scattering experiments

Biophysics and Physicobiology, 2019, Vol.16, pp.377-390

2019

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A theoretical framework for calculations of the structural relaxation time on the basis of the free energy landscape theory

Chemical physics letters, 2013-07, Vol.577, p.58-61

2013

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3D-RISM-AI: A Machine Learning Approach to Predict Protein–Ligand Binding Affinity Using 3D-RISM

Allosteric Regulation of 3CL Protease of SARS-CoV-2 and SARS-CoV Observed in the Crystal Structure Ensemble

Binding and Unbinding Pathways of Peptide Substrates on the SARS-CoV‑2 3CL Protease

Structure of SARS-CoV-2 membrane protein essential for virus assembly

Mechanism of Vitamin D Receptor Ligand-Binding Domain Regulation Studied by gREST Simulations

An accurate and rapid method for calculating hydration free energies of a variety of solutes including proteins

Effect of Water Molecules on the Activating S810L Mutation of the Mineralocorticoid Receptor

A synthetic ion channel with anisotropic ligand response

Elimination of Finite-Size Effects on Binding Free Energies via the Warp-Drive Method

TLR3 forms a laterally aligned multimeric complex along double-stranded RNA for efficient signal transduction

Supramolecular Mechanosensitive Potassium Channel Formed by Fluorinated Amphiphilic Cyclophane

Development of the force field for cyclosporine A

Functional dynamics of SARS-CoV-2 3C-like protease as a member of clan PA

Serine 298 Phosphorylation in Linker 2 of UHRF1 Regulates Ligand-Binding Property of Its Tandem Tudor Domain

Mandibulofacial dysostosis with alopecia results from ETAR gain-of-function mutations via allosteric effects on ligand binding

Structural basis for ligand recognition and signaling of hydroxy-carboxylic acid receptor 2

Imidazolinium‐based Multiblock Amphiphile as Transmembrane Anion Transporter

Comparison of the Molecular Motility of Tubulin Dimeric Isoforms: Molecular Dynamics Simulations and Diffracted X-ray Tracking Study

Apo- and Antagonist-Binding Structures of Vitamin D Receptor Ligand-Binding Domain Revealed by Hybrid Approach Combining Small-Angle X‑ray Scattering and Molecular Dynamics

Rotation Mechanism of Molecular Motor V1-ATPase Studied by Multiscale Molecular Dynamics Simulation

Finite-Size Effect on the Charging Free Energy of Protein in Explicit Solvent

An accurate and efficient computation method of the hydration free energy of a large, complex molecule

Rotational Mechanism Model of the Bacterial V1 Motor Based on Structural and Computational Analyses

Combination of coarse-grained molecular dynamics simulations and small-angle X-ray scattering experiments

A theoretical framework for calculations of the structural relaxation time on the basis of the free energy landscape theory

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