Ryuhei Harada

23 papers Journal 23
YearRankTypeTitle / Venue / Authors
2026 J jnl
DFDD: A Cloud-Ready Tool for Distance-Guided Fully Dynamic Docking in Host-Guest Complexation.
J. Chem. Inf. Model.
Kowit Hengphasatporn, Lian Duan, Ryuhei Harada, Yasuteru Shigeta
2025 J jnl
Construction of PROTAC-Mediated Ternary Complex Structure Distribution Profiles Using Extensive Conformational Search.
J. Chem. Inf. Model.
Genki Kudo, Takumi Hirao, Ryuhei Harada, Yasuteru Shigeta, Takatsugu Hirokawa, Ryunosuke Yoshino
2024 J jnl
BEMM-GEN: A Toolkit for Generating a Biomolecular Environment-Mimicking Model for Molecular Dynamics Simulation.
J. Chem. Inf. Model.
Takunori Yasuda, Rikuri Morita, Yasuteru Shigeta, Ryuhei Harada
2024 J jnl
Evaluating solubility, stability, and inclusion complexation of oxyresveratrol with various β-cyclodextrin derivatives using advanced computational techniques and experimental validation.
Comput. Biol. Chem.
Saba Ali, Aamir Aman, Kowit Hengphasatporn, Lipika Oopkaew, Bunyaporn Todee, Ryo Fujiki, Ryuhei Harada, Yasuteru Shigeta, Kuakarun Krusong, Kiattawee Choowongkomon, Warinthorn Chavasiri, Peter Wolschann, Panupong Mahalapbutr, Thanyada Rungrotmongkol
2024 J jnl
Ribosome Tunnel Environment Drives the Formation of α-Helix during Cotranslational Folding.
J. Chem. Inf. Model.
Takunori Yasuda, Rikuri Morita, Yasuteru Shigeta, Ryuhei Harada
2023 J jnl
Efficient screening of protein-ligand complexes in lipid bilayers using LoCoMock score.
J. Comput. Aided Mol. Des.
Rikuri Morita, Yasuteru Shigeta, Ryuhei Harada
2023 J jnl
Free-Energy Profiles for Membrane Permeation of Compounds Calculated Using Rare-Event Sampling Methods.
J. Chem. Inf. Model.
Ryuhei Harada, Rikuri Morita, Yasuteru Shigeta
2022 J jnl
Protein Structure Validation Derives a Smart Conformational Search in a Physically Relevant Configurational Subspace.
J. Chem. Inf. Model.
Takunori Yasuda, Rikuri Morita, Yasuteru Shigeta, Ryuhei Harada
2022 J jnl
Structural Validation by the
J. Chem. Inf. Model.
Takunori Yasuda, Rikuri Morita, Yasuteru Shigeta, Ryuhei Harada
2020 J jnl
Efficient Conformational Sampling of Collective Motions of Proteins with Principal Component Analysis-Based Parallel Cascade Selection Molecular Dynamics.
J. Chem. Inf. Model.
Takunori Yasuda, Yasuteru Shigeta, Ryuhei Harada
2020 J jnl
Protein Dynamics and the Folding Degree.
J. Chem. Inf. Model.
Vladimír Sládek, Ryuhei Harada, Yasuteru Shigeta
2019 J jnl
Nontargeted Parallel Cascade Selection Molecular Dynamics Based on a Nonredundant Selection Rule for Initial Structures Enhances Conformational Sampling of Proteins.
J. Chem. Inf. Model.
Ryuhei Harada, Vladimír Sládek, Yasuteru Shigeta
2019 J jnl
Selection Rules for Outliers in Outlier Flooding Method Regulate Its Conformational Sampling Efficiency.
J. Chem. Inf. Model.
Ryuhei Harada, Yasuteru Shigeta
2019 J jnl
Temperature-pressure shuffling outlier flooding method enhances the conformational sampling of proteins.
J. Comput. Chem.
Ryuhei Harada, Ryunosuke Yoshino, Hiroaki Nishizawa, Yasuteru Shigeta
2018 J jnl
Temperature-Shuffled Structural Dissimilarity Sampling Based on a Root-Mean-Square Deviation.
J. Chem. Inf. Model.
Ryuhei Harada, Yasuteru Shigeta
2017 J jnl
Common folding processes of mini-proteins: Partial formations of secondary structures initiate the immediate protein folding.
J. Comput. Chem.
Ryuhei Harada, Yu Takano, Yasuteru Shigeta
2017 J jnl
Self-Avoiding Conformational Sampling Based on Histories of Past Conformational Searches.
J. Chem. Inf. Model.
Ryuhei Harada, Yasuteru Shigeta
2017 J jnl
Structural dissimilarity sampling with dynamically self-guiding selection.
J. Comput. Chem.
Ryuhei Harada, Yasuteru Shigeta
2017 J jnl
Temperature-shuffled parallel cascade selection molecular dynamics accelerates the structural transitions of proteins.
J. Comput. Chem.
Ryuhei Harada, Yasuteru Shigeta
2016 J jnl
Sparsity-weighted outlier FLOODing (OFLOOD) method: Efficient rare event sampling method using sparsity of distribution.
J. Comput. Chem.
Ryuhei Harada, Tomotake Nakamura, Yasuteru Shigeta
2015 J jnl
Enhanced conformational sampling method for proteins based on the TaBoo SeArch algorithm: Application to the folding of a mini-protein, chignolin.
J. Comput. Chem.
Ryuhei Harada, Yu Takano, Yasuteru Shigeta
2015 J jnl
Protein folding pathways extracted by OFLOOD: Outlier FLOODing method.
J. Comput. Chem.
Ryuhei Harada, Tomotake Nakamura, Yu Takano, Yasuteru Shigeta
2014 J jnl
On the induced-fit mechanism of substrate-enzyme binding structures of nylon-oligomer hydrolase.
J. Comput. Chem.
Takeshi Baba, Ryuhei Harada, Masayoshi Nakano, Yasuteru Shigeta