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Exhaustive search of the configurational space of heat‐shock protein 90 with its inhibitor by multicanonical molecular dynamics based dynamic docking

Journal of computational chemistry, 2020-06, Vol.41 (17), p.1606-1615

2020

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Thermal stability of single‐domain antibodies estimated by molecular dynamics simulations

Protein science, 2019-02, Vol.28 (2), p.429-438

2019

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Structural basis of mutants of PET‐degrading enzyme from Saccharomonospora viridis AHK190 with high activity and thermal stability

Proteins, structure, function, and bioinformatics, 2021-05, Vol.89 (5), p.502-511

2021

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N‑Terminal-Driven Binding Mechanism of an Antigen Peptide to Human Leukocyte Antigen-A2402 Elucidated by Multicanonical Molecular Dynamic-Based Dynamic Docking and Path Sampling Simulations

The journal of physical chemistry. B, 2021-12, Vol.125 (49), p.13376-13384

2021

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Protein Data Bank Japan: Celebrating our 20th anniversary during a global pandemic as the Asian hub of three dimensional macromolecular structural data

Protein science, 2022-01, Vol.31 (1), p.173-186

2022

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Dynamic Docking Using Multicanonical Molecular Dynamics: Simulating Complex Formation at the Atomistic Level

Methods in molecular biology (Clifton, N.J.), 2021, Vol.2266, p.187

2021

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Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large structures

Nucleic acids research, 2017-01, Vol.45 (D1), p.D282

2017

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Mutual population-shift driven antibody-peptide binding elucidated by molecular dynamics simulations

Scientific reports, 2020-01, Vol.10 (1), p.1406-1406, Article 1406

2020

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New tools and functions in data‐out activities at Protein Data Bank Japan (PDBj)

Protein science, 2018-01, Vol.27 (1), p.95-102

2018

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Advancing the field of computational drug design using multicanonical molecular dynamics-based dynamic docking

Biophysical reviews, 2022-12, Vol.14 (6), p.1349-1358

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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The Biological Structure Model Archive (BSM-Arc): an archive for in silico models and simulations

Biophysical reviews, 2020-04, Vol.12 (2), p.371-375

2020

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Exploring ligand binding pathways on proteins using hypersound-accelerated molecular dynamics

Nature communications, 2021-05, Vol.12 (1), p.2793-10, Article 2793

2021

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Accurate Binding Configuration Prediction of a G‑Protein-Coupled Receptor to Its Antagonist Using Multicanonical Molecular Dynamics-Based Dynamic Docking

Journal of chemical information and modeling, 2021-10, Vol.61 (10), p.5161-5171

2021

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Dynamic Docking of a Medium-Sized Molecule to Its Receptor by Multicanonical MD Simulations

The journal of physical chemistry. B, 2019-03, Vol.123 (11), p.2479-2490

2019

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Elucidation of binding mechanism, affinity, and complex structure between mWT1 tumor‐associated antigen peptide and HLA‐A24:02

Protein science, 2023-10, Vol.32 (10), p.e4775-e4775

2023

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Accurate Prediction of Complex Structure and Affinity for a Flexible Protein Receptor and Its Inhibitor

Journal of chemical theory and computation, 2017-06, Vol.13 (6), p.2389-2399

2017

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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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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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Mutual induced-fit mechanism drives binding between intrinsically disordered Bim and cryptic binding site of Bcl-xL

Communications biology, 2023-03, Vol.6 (1), p.349-349, Article 349

2023

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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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Thermal Stability Estimation of Single Domain Antibodies Using Molecular Dynamics Simulations

Methods in molecular biology (Clifton, N.J.), 2023, Vol.2552, p.151

2023

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Enhanced Coarse-Grained Molecular Dynamics Simulation with a Smoothed Hybrid Potential Using a Neural Network Model

Journal of chemical theory and computation, 2024-01, Vol.20 (1), p.7-17

2024

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Structural and thermodynamic characterization of endo-1,3-β-glucanase: Insights into the substrate recognition mechanism

Biochimica et biophysica acta. Proteins and proteomics, 2018-03, Vol.1866 (3), p.415-425

2018

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Molmil: a molecular viewer for the PDB and beyond

Journal of cheminformatics, 2016-08, Vol.8 (1), p.42-42, Article 42

2016

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Exhaustive search of the configurational space of heat‐shock protein 90 with its inhibitor by multicanonical molecular dynamics based dynamic docking

Thermal stability of single‐domain antibodies estimated by molecular dynamics simulations

Structural basis of mutants of PET‐degrading enzyme from Saccharomonospora viridis AHK190 with high activity and thermal stability

N‑Terminal-Driven Binding Mechanism of an Antigen Peptide to Human Leukocyte Antigen-A2402 Elucidated by Multicanonical Molecular Dynamic-Based Dynamic Docking and Path Sampling Simulations

Protein Data Bank Japan: Celebrating our 20th anniversary during a global pandemic as the Asian hub of three dimensional macromolecular structural data

Dynamic Docking Using Multicanonical Molecular Dynamics: Simulating Complex Formation at the Atomistic Level

Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large structures

Mutual population-shift driven antibody-peptide binding elucidated by molecular dynamics simulations

New tools and functions in data‐out activities at Protein Data Bank Japan (PDBj)

Advancing the field of computational drug design using multicanonical molecular dynamics-based dynamic docking

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

The Biological Structure Model Archive (BSM-Arc): an archive for in silico models and simulations

Exploring ligand binding pathways on proteins using hypersound-accelerated molecular dynamics

Accurate Binding Configuration Prediction of a G‑Protein-Coupled Receptor to Its Antagonist Using Multicanonical Molecular Dynamics-Based Dynamic Docking

Dynamic Docking of a Medium-Sized Molecule to Its Receptor by Multicanonical MD Simulations

Elucidation of binding mechanism, affinity, and complex structure between mWT1 tumor‐associated antigen peptide and HLA‐A24:02

Accurate Prediction of Complex Structure and Affinity for a Flexible Protein Receptor and Its Inhibitor

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

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

Mutual induced-fit mechanism drives binding between intrinsically disordered Bim and cryptic binding site of Bcl-xL

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

Thermal Stability Estimation of Single Domain Antibodies Using Molecular Dynamics Simulations

Enhanced Coarse-Grained Molecular Dynamics Simulation with a Smoothed Hybrid Potential Using a Neural Network Model

Structural and thermodynamic characterization of endo-1,3-β-glucanase: Insights into the substrate recognition mechanism

Molmil: a molecular viewer for the PDB and beyond

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