HARADA Ryuhei
- Articles
- Free-energy Profiles for Membrane Permeation of Compounds Calculated Using Rare-Event Sampling Methods
Harada Ryuhei; Morita Rikuri; Shigeta Yasuteru
JOURNAL OF CHEMICAL INFORMATION AND MODELING/63(1)/pp.259-269, 2023-01 - Efficient Screening of Protein-Ligand Complexes in Lipid Bilayers Using LoCoMock Score
Morita Rikuri; Shigeta Yasuteru; Harada Ryuhei
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN/37(4)/pp.217-225, 2023-03 - 4-hydroxyphenylpyruvate dioxygenase (HPPD)における金属活性中心の力場パラメータの構築とその評価
宗井 陽平; 堀 優太; Kowit Hengphasatporn; 原田 隆平; 重田 育照
Journal of Computer Chemistry, Japan/21(4)/pp.82-84, 2023-03 - Autism-associated mutation in Hevin/Sparcl1 induces endoplasmic reticulum stress through structural instability
Takumi Taketomi; Yasuda Takunori; Morita Rikuri; Kim ...
bioRxiv/12(1), 2022-04-13 - Structural Validation by the G-Factor Properly Regulates Boost Potentials Imposed in Conformational Sampling of Proteins
Yasuda Takunori; Morita Rikuri; Shigeta Yasuteru; Harada ...
JOURNAL OF CHEMICAL INFORMATION AND MODELING/62(14)/pp.3442-3452, 2022-07 - The role of ATP in solubilizing RNA-binding protein fused in sarcoma
Aida Hayato; Shigeta Yasuteru; Harada Ryuhei
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS/90(8)/pp.1606-1612, 2022-08 - Ligand Binding Path Sampling Based on Parallel Cascade Selection Molecular Dynamics: LB-PaCS-MD
Aida Hayato; Shigeta Yasuteru; Harada Ryuhei
Materials/15(4), 2022-02 - Histone H3 Inhibits Ubiquitin-Ubiquitin Intermolecular Interactions to Enhance Binding to DNA Methyl Transferase 1
Yasuda Takunori; Morita Rikuri; Shigeta Yasuteru; Harada ...
JOURNAL OF MOLECULAR BIOLOGY/434(2), 2022-01-30 - Residue Folding Degree-Relationship to Secondary Structure Categories and Use as Collective Variable
Sladek Vladimir; Harada Ryuhei; Shigeta Yasuteru
International Journal of Molecular Sciences/22(23)/p.13042, 2021-12 - Structural Variations of Metallothionein with or without Zinc Ions Elucidated by All-Atom Molecular Dynamics Simulations
Morita Rikuri; Shigeta Yasuteru; Harada Ryuhei
The journal of physical chemistry. B/125(46)/pp.12712-12717, 2021-11-25 - A post-process to estimate an approximated minimal free energy path based on local centroids
Morita Rikuri; Shigeta Yasuteru; Harada Ryuhei
CHEMICAL PHYSICS LETTERS/782, 2021-11 - Integrate in silico studies on the role of nicotinamide adenine dinucleotide (NADH) binding in activating C-terminal binding protein 2 (CtBP2)
Tsukasa Aoyagi; Yoshino Ryunosuke; Yuki Mitsuta; Rikuri ...
Chemistry Letters/51(1)/pp.1-4, 2021-10 - Solubility and Membrane Permeability of Cyclic Dipeptides Approximately Estimated by Quantum Chemistry and Molecular Dynamics Calculations
Yanagi Koki; Mitsuta Yuki; Takaoka Kenta; Takahashi Teru...
Chemistry Letters/50(12)/pp.1964-1967, 2021-09 - Independent Nontargeted Parallel Cascade Selection Molecular Dynamics (Ino-PaCS-MD) to Enhance the Conformational Sampling of Proteins
Yasuda Takunori; Morita Rikuri; Shigeta Yasuteru; Harada ...
JOURNAL OF CHEMICAL THEORY AND COMPUTATION/17(9)/pp.5933-5943, 2021-09 - In silico mutational analyses reveal different ligand-binding abilities of double pockets of medaka fish taste receptor type 1 essential for efficient taste recognition
Aida Hayato; Morita Rikuri; Shigeta Yasuteru; Harada Ryuhei
PHYSICAL CHEMISTRY CHEMICAL PHYSICS/23(36)/pp.20398-20405, 2021-09 - Phosphorylation in the accessory domain of yeast histone chaperone protein 1 exposes the nuclear export signal sequence
Ashida Sho; Morita Rikuri; Shigeta Yasuteru; Harada Ryuhei
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS/Epub, 2021-09 - pyProGA-A PyMOL plugin for protein residue network analysis
Sladek Vladimir; Yamamoto Yuta; Harada Ryuhei; Shoji ...
PLOS ONE/16(7), 2021-07 - Split conformation of Chaetomium thermophilum Hsp104 disaggregase
Inoue Yosuke; Hanazono Yuya; Noi Kentaro; Kawamoto Ak...
Structure (London, England : 1993)/29(7)/pp.1-10, 2021-07 - Comprehensive predictions of secondary structures for comparative analysis in different species
Morita Rikuri; Shigeta Yasuteru; Harada Ryuhei
Journal of structural biology/213(2), 2021-06-01 - 環状ペプチドの膜透過における溶媒和自由エネルギー計算
栁 昂輝; 原田 隆平; 満田 祐樹; 重田育照
Journal of Computational Chemistry Japan/19(4)/pp.125-127, 2021-03 - Comprehensive Analysis of Intrinsically Disordered Regions to Elucidate Their Physical Properties using a Modified Parameter
Aida Hayato; Harada Ryuhei; Shigeta Yasuteru; Tomii K...
BIOPHYSICAL JOURNAL/120(3::1)/pp.216A-216A, 2021-02 - Rearrangements of Water Molecules in Parallel Cascade Selection Molecular Dynamics Enhance Structural Explorations of Proteins
Morita Rikuri; Shigeta Yasuteru; Harada Ryuhei
Bulletin of the Chemical Society of Japan/94(1)/pp.97-105, 2021-01 - The Folding of Trp-cage is Regulated by Stochastic Flip of the Side Chain of Tryptophan
Yasuda Takunori; Shigeta Yasuteru; Harada Ryuhei
CHEMISTRY LETTERS/50(1)/pp.162-165, 2021-01 - Enhanced Conformational Sampling Method Based on Anomaly Detection Parallel Cascade Selection Molecular Dynamics: ad-PaCS-MD
Harada Ryuhei; Yamaguchi Kota; Shigeta Yasuteru
Journal of chemical theory and computation/16(10)/pp.6716-6725, 2020-10 - Molecular Mechanism for the Actin-Binding Domain of alpha-Actinin Ain1 Elucidated by Molecular Dynamics Simulations and Mutagenesis Experiments
Morita Rikuri; Nakano Kentaro; Shigeta Yasuteru; Harada ...
JOURNAL OF PHYSICAL CHEMISTRY B/124(39)/pp.8495-8503, 2020-10 - more...
- Free-energy Profiles for Membrane Permeation of Compounds Calculated Using Rare-Event Sampling Methods