HARADA Ryuhei

Researcher's full information

Articles

• Effects of Antifreezing Protein from Rhagium inquisitor Binding on Ice Growth: A Molecular Dynamics Study
  Kimatsuka Masato; Sato Ryuma; Harada Ryuhei; Shoji Mitsu...
  Chemistry Letters/48(3)/pp.223-226, 2019-03
  
  CiNii
• Temperature-pressure shuffling outlier flooding method enhances the conformational sampling of proteins
  Harada Ryuhei; Yoshino Ryunosuke; Nishizawa Hiroaki; Shig...
  Journal of computational chemistry/40(15)/pp.1530-1537, 2019-02
  
  PubMed
• Hybrid Cascade-Type Molecular Dynamics with a Markov State Model for Efficient Free Energy Calculations
  Harada Ryuhei; Shigeta Yasuteru
  JOURNAL OF CHEMICAL THEORY AND COMPUTATION/15(1)/pp.680-687, 2019-01
  
  PubMed
• Simple, yet Efficient Conformational Sampling Methods for Reproducing/Predicting Biologically Rare Events of Proteins
  Harada Ryuhei
  Bulletin of the Chemical Society of Japan/91(9)/pp.1436-1450, 2018-09
  
  CiNii
• Selection rules on initial structures in parallel cascade selection molecular dynamics affect conformational sampling efficiency
  Harada Ryuhei; Shigeta Yasuteru
  Journal of molecular graphics & modelling/85/pp.153-159, 2018-09
  
  PubMed
• How Does Friction Coefficient Affect the Conformational Sampling Efficiency of Parallel Cascade Selection Molecular Dynamics?
  Harada Ryuhei; Shigeta Yasuteru
  Chemistry Letters/47(9)/pp.1119-1122, 2018-09
  
  CiNii
• Temperature-Shuffled Structural Dissimilarity Sampling Based on a Root-Mean-Square Deviation
  Harada Ryuhei; Shigeta Yasuteru
  Journal of chemical information and modeling/58(7)/pp.1397-1405, 2018-07
  
  PubMed
• How low-resolution structural data predict the conformational changes of a protein: a study on data-driven molecular dynamics simulations
  Harada Ryuhei; Shigeta Yasuteru
  Physical chemistry chemical physics : PCCP/20(26)/pp.17790-17798, 2018-06
  
  PubMed
• On-the-Fly Specifications of Reaction Coordinates in Parallel Cascade Selection Molecular Dynamics Accelerate Conformational Transitions of Proteins
  Harada Ryuhei; Shigeta Yasuteru
  Journal of chemical theory and computation/14(6)/pp.3332-3341, 2018-05
  
  PubMed
• Coulomb and CH-π interactions in (6-4) photolyase-DNA complex dominate DNA binding and repair abilities
  Terai Yuma; Sato Ryuma; Yumiba Takahiro; Harada Ryuhei; S...
  Nucleic acids research/Epub, 2018-05
  
  PubMed
• Free energy calculation method based on the parallel cascade selection molecular dynamics simulation combined with Markov state model
  原田 隆平; 重田 育照
  Meeting Abstracts of the Physical Society of Japan/73/pp.2525-2525, 2018
  
  CiNii
• Developments of Efficient Conformational Sampling Methods for Reproducing and Predicting Biologically Relevant Rare Events of Proteins
  原田 隆平; 重田 育照
  Meeting Abstracts of the Physical Society of Japan/73/pp.3010-3010, 2018
  
  CiNii
• The Formation of Hydrophobic Core Regulates the Protein Folding of Villin Elucidated with Parallel Cascade Selection Molecular Dynamics
  Harada Ryuhei; Aida Hayato; Shigeta Yasuteru
  Chemistry Letters/47(10)/pp.1300-1303, 2018
  
  CiNii
• Analyses on Dynamical Ordering of Protein Functions by Means of Cascade Selection Molecular Dynamics
  原田 隆平; 重田 育照
  Journal of Computer Chemistry, Japan/17(1)/pp.46-56, 2018
  
  CiNii
• Programed dynamical ordering in self-organization processes of a nanocube: a molecular dynamics study
  Harada Ryuhei; Mashiko Takako; Tachikawa Masanori; Hiraok...
  Physical chemistry chemical physics : PCCP/20(14)/pp.9115-9122, 2018-04
  
  PubMed