HARADA Ryuhei

Researcher's full information

Articles

• 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
  
  PubMed
• 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
  
  PubMed
• 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
  
  PubMed
• 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
  
  PubMed
• 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
  
  PubMed
• 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
  
  PubMed
• カスケード選択型分子動力学シミュレーションで実現する環状ペプチドの膜透過シミュレーション
  原田 隆平
  スーパーコンピューティングニュース 特集号/22(1)/pp.13-18, 2020-08
• Efficient Conformational Sampling of Collective Motions of Proteins with Principal Component Analysis-Based Parallel Cascade Selection Molecular Dynamics
  Yasuda Takunori; Shigeta Yasuteru; Harada Ryuhei
  Journal of chemical information and modeling/60(8)/pp.4021-4029, 2020-08
  
  PubMed
• Regenerations of Initial Velocities in Parallel Cascade Selection Molecular Dynamics (PaCS-MD) Enhance the Conformational Transitions of Proteins
  Aida Hayato; Shigeta Yasuteru; Harada Ryuhei
  Chemistry Letters/49(7)/pp.798-801, 2020-04
  
  CiNii
• The Dynamics of S-adenosyl-methionine and S-adenosyl-homocysteine in Mouse Dnmt1 is Driven by Their Structural Flexibilities
  Yasuda Takunori; Shigeta Yasuteru; Harada Ryuhei
  Chemistry Letters/49(7)/pp.785-788, 2020-04
  
  CiNii
• Distribution of Conter Ions in Negatively-charged Lipid/Water/Air Interface: Molecular Dynamics Study
  Takahashi T.; Harada R.; Shigeta Yasuteru
  Chemistry Letters/4(49)/pp.361-363, 2020-04
• Protein Dynamics and the Folding Degree
  Vladimir Sladek; Harada Ryuhei; Shigeta Yasuteru
  Journal of Chemical Information and Modeling/60(3)/pp.1559-1567, 2020-03
  
  PubMed
• more...