HARADA Ryuhei

Researcher's full information

Articles

• 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
• タンパク質の機能発現に重要なレアイベントを抽出するサンプリング手法の開発
  原田 隆平
  分子シミュレーション学会誌 アンサンブル/22(1)/pp.1-6, 2020-01
• Rare Event Sampling of Biomolecules Based on Distributed Computing
  原田 隆平
  BUTSURI/75(1)/pp.28-33, 2020-01
  
  CiNii
• Developments of Rare Event Sampling Methods for Proteins
  原田 隆平; Sladek Vladimir; 重田育照
  Journal of Computational Chemistry Japan/18(5)/pp.199-201, 2019-12
  
  CiNii
• Nontargeted Parallel Cascade Selection Molecular Dynamics Based on a Nonredundant Selection Rule for Initial Structures Enhances Conformational Sampling of Proteins
  Harada Ryuhei; Vladimir Sladek; Yasuteru Shigeta
  Journal of Chemical Information and Modeling/59(12)/p.5198, 2019-11
• Nontargeted Parallel Cascade Selection Molecular Dynamics Using Time-Localized Prediction of Conformational Transitions in Protein Dynamics
  Harada Ryuhei; Sladek Vladimir; Shigeta Yasuteru
  JOURNAL OF CHEMICAL THEORY AND COMPUTATION/15(9)/pp.5144-5153, 2019-09
  
  PubMed
• Selection Rules for Outliers in Outlier Flooding Method Regulate Its Conformational Sampling Efficiency
  Harada Ryuhei; Shigeta Yasuteru
  JOURNAL OF CHEMICAL INFORMATION AND MODELING/59(9)/pp.3919-3926, 2019-09
  
  PubMed
• カスケード選択型分子動力学シミュレーションに基づく低解像度タンパク質構造の精密化
  原田 隆平
  スーパーコンピューティングニュース特集号/21(1)/pp.5-9, 2019-08
• Parallel cascade selection molecular dynamics to screen for protein complexes generated by rigid docking
  Harada Ryuhei; Yoshino Ryunosuke; Nishizawa Hiroaki; Shig...
  Journal of molecular graphics & modelling/92/pp.94-99, 2019-07
  
  PubMed
• Possible Configurations of Apo-form Taste Receptor Type 1 (T1r) Studied by Microsecond-order Molecular Dynamics Simulation
  Aida Hayato; Harada Ryuhei; Shigeta Yasuteru
  Chemistry Letters/48(4)/pp.325-328, 2019-04
  
  CiNii
• Molecular Dynamics studies on the effects of Antifreezing Protein from Rhagium inquisitor (RiAFP) on Ice Growth
  木間塚政人; 佐藤竜馬; 原田隆平; 庄司 光男; 重田 育照
  Journal of Computer Chemistry, Japan/17(5)/pp.222-224, 2019-03
  
  CiNii Tsukuba Repository
• 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
• more...