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Free-Energy Profiles for Membrane Permeation of Compounds Calculated Using Rare-Event Sampling Methods

Journal of chemical information and modeling, 2023-01, Vol.63 (1), p.259-269

2023

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A post-process to estimate an approximated minimal free energy path based on local centroids

Chemical physics letters, 2021-11, Vol.782, p.139003, Article 139003

2021

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Cell cycle-dependent phosphorylation of IQGAP is involved in assembly and stability of the contractile ring in fission yeast

Biochemical and biophysical research communications, 2021-01, Vol.534, p.1026-1032

2021

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Structural Validation by the G‑Factor Properly Regulates Boost Potentials Imposed in Conformational Sampling of Proteins

Journal of chemical information and modeling, 2022-07, Vol.62 (14), p.3442-3452

2022

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Protein Structure Validation Derives a Smart Conformational Search in a Physically Relevant Configurational Subspace

Journal of chemical information and modeling, 2022-12, Vol.62 (23), p.6217-6227

2022

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Rearrangements of Water Molecules in Parallel Cascade Selection Molecular Dynamics Enhance Structural Explorations of Proteins

Bulletin of the Chemical Society of Japan, 2021-01, Vol.94 (1), p.97-105

2021

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Efficient screening of protein-ligand complexes in lipid bilayers using LoCoMock score

Journal of computer-aided molecular design, 2023-04, Vol.37 (4), p.217-225

2023

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Autism-associated mutation in Hevin/Sparcl1 induces endoplasmic reticulum stress through structural instability

Scientific reports, 2022-07, Vol.12 (1), p.11891-11891, Article 11891

2022

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Comprehensive predictions of secondary structures for comparative analysis in different species

Journal of structural biology, 2021-06, Vol.213 (2), p.107735-107735, Article 107735

2021

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Integrated In Silico Studies on the Role of Nicotinamide Adenine Dinucleotide (NADH) Binding in Activating C-Terminal Binding Protein 2 (CtBP2)

Chemistry letters, 2022-01, Vol.51 (1), p.1-4

2022

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Molecular dissection of the actin-binding ability of the fission yeast α-actinin, Ain1, in vitro and in vivo

Journal of biochemistry (Tokyo), 2017-08, Vol.162 (2), p.93-102

2017

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Latrunculin resistance mechanism of non‐conventional actin NAP1 uncovered by molecular dynamics simulations

Cytoskeleton (Hoboken, N.J.), 2024-02, Vol.81 (2-3), p.143-150

2024

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Structural Variations of Metallothionein with or without Zinc Ions Elucidated by All-Atom Molecular Dynamics Simulations

The journal of physical chemistry. B, 2021-11, Vol.125 (46), p.12712-12717

2021

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Structural Fluctuation in Homodimeric Aminoacyl-tRNA Synthetases Induces Half-of-the-Sites Activity

The journal of physical chemistry. B, 2024-11, Vol.128 (44), p.10823-10830

2024

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Ribosome Tunnel Environment Drives the Formation of α‑Helix during Cotranslational Folding

Journal of chemical information and modeling, 2024-08, Vol.64 (16), p.6610-6622

2024

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BEMM-GEN: A Toolkit for Generating a Biomolecular Environment-Mimicking Model for Molecular Dynamics Simulation

Journal of chemical information and modeling, 2024-10, Vol.64 (19), p.7184-7188

2024

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Histone H3 Inhibits Ubiquitin-Ubiquitin Intermolecular Interactions to Enhance Binding to DNA Methyl Transferase 1

Journal of molecular biology, 2022-01, Vol.434 (2), p.167371-167371, Article 167371

2022

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Phosphorylation in the accessory domain of yeast histone chaperone protein 1 exposes the nuclear export signal sequence

Proteins, structure, function, and bioinformatics, 2022-02, Vol.90 (2), p.317-321

2022

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Independent Nontargeted Parallel Cascade Selection Molecular Dynamics (Ino-PaCS-MD) to Enhance the Conformational Sampling of Proteins

Journal of chemical theory and computation, 2021-09, Vol.17 (9), p.5933-5943

2021

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mutational analyses reveal different ligand-binding abilities of double pockets of medaka fish taste receptor type 1 essential for efficient taste recognition

Physical chemistry chemical physics : PCCP, 2021-09, Vol.23 (36), p.2398-245

2021

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In silico mutational analyses reveal different ligand-binding abilities of double pockets of medaka fish taste receptor type 1 essential for efficient taste recognition

Physical chemistry chemical physics : PCCP, 2021-09, Vol.23 (36), p.20398-20405

2021

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Molecular Mechanism for the Actin-Binding Domain of α‑Actinin Ain1 Elucidated by Molecular Dynamics Simulations and Mutagenesis Experiments

The journal of physical chemistry. B, 2020-10, Vol.124 (39), p.8495-8503

2020

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Drug-discovery Simulation for Membrane Proteins

Seibutsu Butsuri, 2024, Vol.64(1), pp.21-24

2024

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Free-Energy Profiles for Membrane Permeation of Compounds Calculated Using Rare-Event Sampling Methods

A post-process to estimate an approximated minimal free energy path based on local centroids

Cell cycle-dependent phosphorylation of IQGAP is involved in assembly and stability of the contractile ring in fission yeast

Structural Validation by the G‑Factor Properly Regulates Boost Potentials Imposed in Conformational Sampling of Proteins

Protein Structure Validation Derives a Smart Conformational Search in a Physically Relevant Configurational Subspace

Rearrangements of Water Molecules in Parallel Cascade Selection Molecular Dynamics Enhance Structural Explorations of Proteins

Efficient screening of protein-ligand complexes in lipid bilayers using LoCoMock score

Autism-associated mutation in Hevin/Sparcl1 induces endoplasmic reticulum stress through structural instability

Comprehensive predictions of secondary structures for comparative analysis in different species

Integrated In Silico Studies on the Role of Nicotinamide Adenine Dinucleotide (NADH) Binding in Activating C-Terminal Binding Protein 2 (CtBP2)

Identifying antibiotics based on structural differences in the conserved allostery from mitochondrial heme-copper oxidases

Author Correction: Identifying antibiotics based on structural differences in the conserved allostery from mitochondrial heme-copper oxidases

Molecular dissection of the actin-binding ability of the fission yeast α-actinin, Ain1, in vitro and in vivo

Latrunculin resistance mechanism of non‐conventional actin NAP1 uncovered by molecular dynamics simulations

Structural Variations of Metallothionein with or without Zinc Ions Elucidated by All-Atom Molecular Dynamics Simulations

Structural Fluctuation in Homodimeric Aminoacyl-tRNA Synthetases Induces Half-of-the-Sites Activity

Ribosome Tunnel Environment Drives the Formation of α‑Helix during Cotranslational Folding

BEMM-GEN: A Toolkit for Generating a Biomolecular Environment-Mimicking Model for Molecular Dynamics Simulation

Histone H3 Inhibits Ubiquitin-Ubiquitin Intermolecular Interactions to Enhance Binding to DNA Methyl Transferase 1

Phosphorylation in the accessory domain of yeast histone chaperone protein 1 exposes the nuclear export signal sequence

Independent Nontargeted Parallel Cascade Selection Molecular Dynamics (Ino-PaCS-MD) to Enhance the Conformational Sampling of Proteins

mutational analyses reveal different ligand-binding abilities of double pockets of medaka fish taste receptor type 1 essential for efficient taste recognition

In silico mutational analyses reveal different ligand-binding abilities of double pockets of medaka fish taste receptor type 1 essential for efficient taste recognition

Molecular Mechanism for the Actin-Binding Domain of α‑Actinin Ain1 Elucidated by Molecular Dynamics Simulations and Mutagenesis Experiments

Drug-discovery Simulation for Membrane Proteins

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