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ORCIDRyuhei Harada
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2020 – today
- 2024
[j21]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: 108111 (2024)- [j20]Takunori Yasuda, Rikuri Morita, Yasuteru Shigeta, Ryuhei Harada:
Ribosome Tunnel Environment Drives the Formation of α-Helix during Cotranslational Folding. J. Chem. Inf. Model. 64(16): 6610-6622 (2024) - [j19]Takunori Yasuda, Rikuri Morita, Yasuteru Shigeta, Ryuhei Harada:
BEMM-GEN: A Toolkit for Generating a Biomolecular Environment-Mimicking Model for Molecular Dynamics Simulation. J. Chem. Inf. Model. 64(19): 7184-7188 (2024) - 2023
- [j18]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): 217-225 (2023) - [j17]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): 259-269 (2023) - 2022
- [j16]Takunori Yasuda, Rikuri Morita, Yasuteru Shigeta, Ryuhei Harada:
Structural Validation by the G-Factor Properly Regulates Boost Potentials Imposed in Conformational Sampling of Proteins. J. Chem. Inf. Model. 62(14): 3442-3452 (2022) - [j15]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): 6217-6227 (2022) - 2020
- [j14]Vladimír Sládek, Ryuhei Harada, Yasuteru Shigeta:
Protein Dynamics and the Folding Degree. J. Chem. Inf. Model. 60(3): 1559-1567 (2020) - [j13]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): 4021-4029 (2020)
2010 – 2019
- 2019
- [j12]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): 1530-1537 (2019) - [j11]Ryuhei Harada, Yasuteru Shigeta:
Selection Rules for Outliers in Outlier Flooding Method Regulate Its Conformational Sampling Efficiency. J. Chem. Inf. Model. 59(9): 3919-3926 (2019) - [j10]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): 5198-5206 (2019) - 2018
- [j9]Ryuhei Harada, Yasuteru Shigeta:
Temperature-Shuffled Structural Dissimilarity Sampling Based on a Root-Mean-Square Deviation. J. Chem. Inf. Model. 58(7): 1397-1405 (2018) - 2017
- [j8]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): 790-797 (2017) - [j7]Ryuhei Harada, Yasuteru Shigeta:
Structural dissimilarity sampling with dynamically self-guiding selection. J. Comput. Chem. 38(22): 1921-1929 (2017) - [j6]Ryuhei Harada, Yasuteru Shigeta:
Temperature-shuffled parallel cascade selection molecular dynamics accelerates the structural transitions of proteins. J. Comput. Chem. 38(31): 2671-2674 (2017) - [j5]Ryuhei Harada, Yasuteru Shigeta:
Self-Avoiding Conformational Sampling Based on Histories of Past Conformational Searches. J. Chem. Inf. Model. 57(12): 3070-3078 (2017) - 2016
- [j4]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): 724-738 (2016) - 2015
- [j3]Ryuhei Harada, Tomotake Nakamura, Yu Takano, Yasuteru Shigeta:
Protein folding pathways extracted by OFLOOD: Outlier FLOODing method. J. Comput. Chem. 36(2): 97-102 (2015) - [j2]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): 763-772 (2015) - 2014
- [j1]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): 1240-1247 (2014)
Coauthor Index
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