Ryuhei Harada

Publication Activity (10 Years)

Years Active: 2014-2024
Publications (10 Years): 18

Top Topics

Sampling Methods

Experimentally Determined

Top Venues

J. Chem. Inf. Model.

J. Comput. Chem.

Comput. Biol. Chem.

J. Comput. Aided Mol. Des.

Publications

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
Evaluating solubility, stability, and inclusion complexation of oxyresveratrol with various β-cyclodextrin derivatives using advanced computational techniques and experimental validation. Comput. Biol. Chem. 112 (2024)
Ryuhei Harada, Rikuri Morita, Yasuteru Shigeta
Free-Energy Profiles for Membrane Permeation of Compounds Calculated Using Rare-Event Sampling Methods. J. Chem. Inf. Model. 63 (1) (2023)
Rikuri Morita, Yasuteru Shigeta, Ryuhei Harada
Efficient screening of protein-ligand complexes in lipid bilayers using LoCoMock score. J. Comput. Aided Mol. Des. 37 (4) (2023)
Takunori Yasuda, Rikuri Morita, Yasuteru Shigeta, Ryuhei Harada
-Factor Properly Regulates Boost Potentials Imposed in Conformational Sampling of Proteins. J. Chem. Inf. Model. 62 (14) (2022)
Takunori Yasuda, Rikuri Morita, Yasuteru Shigeta, Ryuhei Harada
Protein Structure Validation Derives a Smart Conformational Search in a Physically Relevant Configurational Subspace. J. Chem. Inf. Model. 62 (23) (2022)
Takunori Yasuda, Yasuteru Shigeta, Ryuhei Harada
Efficient Conformational Sampling of Collective Motions of Proteins with Principal Component Analysis-Based Parallel Cascade Selection Molecular Dynamics. J. Chem. Inf. Model. 60 (8) (2020)
Vladimír Sládek, Ryuhei Harada, Yasuteru Shigeta
Protein Dynamics and the Folding Degree. J. Chem. Inf. Model. 60 (3) (2020)
Ryuhei Harada, Vladimír Sládek, Yasuteru Shigeta
Nontargeted Parallel Cascade Selection Molecular Dynamics Based on a Nonredundant Selection Rule for Initial Structures Enhances Conformational Sampling of Proteins. J. Chem. Inf. Model. 59 (12) (2019)
Ryuhei Harada, Ryunosuke Yoshino, Hiroaki Nishizawa, Yasuteru Shigeta
Temperature-pressure shuffling outlier flooding method enhances the conformational sampling of proteins. J. Comput. Chem. 40 (15) (2019)
Ryuhei Harada, Yasuteru Shigeta
Selection Rules for Outliers in Outlier Flooding Method Regulate Its Conformational Sampling Efficiency. J. Chem. Inf. Model. 59 (9) (2019)
Ryuhei Harada, Yasuteru Shigeta
Temperature-Shuffled Structural Dissimilarity Sampling Based on a Root-Mean-Square Deviation. J. Chem. Inf. Model. 58 (7) (2018)
Ryuhei Harada, Yu Takano, Yasuteru Shigeta
Common folding processes of mini-proteins: Partial formations of secondary structures initiate the immediate protein folding. J. Comput. Chem. 38 (11) (2017)
Ryuhei Harada, Yasuteru Shigeta
Temperature-shuffled parallel cascade selection molecular dynamics accelerates the structural transitions of proteins. J. Comput. Chem. 38 (31) (2017)
Ryuhei Harada, Yasuteru Shigeta
Self-Avoiding Conformational Sampling Based on Histories of Past Conformational Searches. J. Chem. Inf. Model. 57 (12) (2017)
Ryuhei Harada, Yasuteru Shigeta
Structural dissimilarity sampling with dynamically self-guiding selection. J. Comput. Chem. 38 (22) (2017)
Ryuhei Harada, Tomotake Nakamura, Yasuteru Shigeta
Sparsity-weighted outlier FLOODing (OFLOOD) method: Efficient rare event sampling method using sparsity of distribution. J. Comput. Chem. 37 (8) (2016)
Ryuhei Harada, Tomotake Nakamura, Yu Takano, Yasuteru Shigeta
Protein folding pathways extracted by OFLOOD: Outlier FLOODing method. J. Comput. Chem. 36 (2) (2015)
Ryuhei Harada, Yu Takano, Yasuteru Shigeta
Enhanced conformational sampling method for proteins based on the TaBoo SeArch algorithm: Application to the folding of a mini-protein, chignolin. J. Comput. Chem. 36 (10) (2015)
Takeshi Baba, Ryuhei Harada, Masayoshi Nakano, Yasuteru Shigeta
On the induced-fit mechanism of substrate-enzyme binding structures of nylon-oligomer hydrolase. J. Comput. Chem. 35 (16) (2014)