HARADA Ryuhei
- Articles
- 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 - 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 - 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 - 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 - 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 - 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 - 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 - 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 - 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 - 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 - 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 - 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 - 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 - 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 - 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 - 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 - 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 - 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 - 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 - 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 - 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 - 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
- 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