On the induced-fit mechanism of substrate-enzyme binding structures of nylon-oligomer hydrolase. - Takeshi Baba; Ryuhei Harada; Masayoshi Nakano; Yasuteru Shigeta (J. Comput. Chem., 2014)

Protein folding pathways extracted by OFLOOD: Outlier FLOODing method. - Ryuhei Harada; Tomotake Nakamura; Yu Takano; Yasuteru Shigeta (J. Comput. Chem., 2015)

Enhanced conformational sampling method for proteins based on the TaBoo SeArch algorithm: Application to the folding of a mini-protein, chignolin. - Ryuhei Harada; Yu Takano; Yasuteru Shigeta (J. Comput. Chem., 2015)

Sparsity-weighted outlier FLOODing (OFLOOD) method: Efficient rare event sampling method using sparsity of distribution. - Ryuhei Harada; Tomotake Nakamura; Yasuteru Shigeta (J. Comput. Chem., 2016)

Structural dissimilarity sampling with dynamically self-guiding selection. - Ryuhei Harada; Yasuteru Shigeta (J. Comput. Chem., 2017)

Temperature-shuffled parallel cascade selection molecular dynamics accelerates the structural transitions of proteins. - Ryuhei Harada; Yasuteru Shigeta (J. Comput. Chem., 2017)

Common folding processes of mini-proteins: Partial formations of secondary structures initiate the immediate protein folding. - Ryuhei Harada; Yu Takano; Yasuteru Shigeta (J. Comput. Chem., 2017)

Self-Avoiding Conformational Sampling Based on Histories of Past Conformational Searches. - Ryuhei Harada; Yasuteru Shigeta (J. Chem. Inf. Model., 2017)

Temperature-Shuffled Structural Dissimilarity Sampling Based on a Root-Mean-Square Deviation. - Ryuhei Harada; Yasuteru Shigeta (J. Chem. Inf. Model., 2018)

Temperature-pressure shuffling outlier flooding method enhances the conformational sampling of proteins. - Ryuhei Harada; Ryunosuke Yoshino; Hiroaki Nishizawa; Yasuteru Shigeta (J. Comput. Chem., 2019)

Selection Rules for Outliers in Outlier Flooding Method Regulate Its Conformational Sampling Efficiency. - Ryuhei Harada; Yasuteru Shigeta (J. Chem. Inf. Model., 2019)

Nontargeted Parallel Cascade Selection Molecular Dynamics Based on a Nonredundant Selection Rule for Initial Structures Enhances Conformational Sampling of Proteins. - Ryuhei Harada; Vladimír Sládek; Yasuteru Shigeta (J. Chem. Inf. Model., 2019)

Protein Dynamics and the Folding Degree. - Vladimír Sládek; Ryuhei Harada; Yasuteru Shigeta (J. Chem. Inf. Model., 2020)

Efficient Conformational Sampling of Collective Motions of Proteins with Principal Component Analysis-Based Parallel Cascade Selection Molecular Dynamics. - Takunori Yasuda; Yasuteru Shigeta; Ryuhei Harada (J. Chem. Inf. Model., 2020)

Structural Validation by the G-Factor Properly Regulates Boost Potentials Imposed in Conformational Sampling of Proteins. - Takunori Yasuda; Rikuri Morita; Yasuteru Shigeta; Ryuhei Harada (J. Chem. Inf. Model., 2022)

Protein Structure Validation Derives a Smart Conformational Search in a Physically Relevant Configurational Subspace. - Takunori Yasuda; Rikuri Morita; Yasuteru Shigeta; Ryuhei Harada (J. Chem. Inf. Model., 2022)

Efficient screening of protein-ligand complexes in lipid bilayers using LoCoMock score. - Rikuri Morita; Yasuteru Shigeta; Ryuhei Harada (J. Comput. Aided Mol. Des., 2023)

Free-Energy Profiles for Membrane Permeation of Compounds Calculated Using Rare-Event Sampling Methods. - Ryuhei Harada; Rikuri Morita; Yasuteru Shigeta (J. Chem. Inf. Model., 2023)

Evaluating solubility, stability, and inclusion complexation of oxyresveratrol with various β-cyclodextrin derivatives using advanced computational techniques and experimental validation. - Saba Ali; Aamir Aman; Kowit Hengphasatporn; Lipika Oopkaew; Bunyaporn Todee; Ryo Fujiki; Ryuhei Harada; Yasuteru Shigeta; Kuakarun Krusong; Kiattawee Choowongkomon; Warinthorn Chavasiri; Peter Wolschann; et al. (Comput. Biol. Chem., 2024)

Ribosome Tunnel Environment Drives the Formation of α-Helix during Cotranslational Folding. - Takunori Yasuda; Rikuri Morita; Yasuteru Shigeta; Ryuhei Harada (J. Chem. Inf. Model., 2024)

BEMM-GEN: A Toolkit for Generating a Biomolecular Environment-Mimicking Model for Molecular Dynamics Simulation. - Takunori Yasuda; Rikuri Morita; Yasuteru Shigeta; Ryuhei Harada (J. Chem. Inf. Model., 2024)

Construction of PROTAC-Mediated Ternary Complex Structure Distribution Profiles Using Extensive Conformational Search. - Genki Kudo; Takumi Hirao; Ryuhei Harada; Yasuteru Shigeta; Takatsugu Hirokawa; Ryunosuke Yoshino (J. Chem. Inf. Model., 2025)