原田 隆平(ハラダ リュウヘイ)
- 論文
- 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
日本コンピュータ化学会/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 - 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 - 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 - 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 - 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 - 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 - 分散型シミュレーションを用いて生体分子のレアイベントを捉える
原田 隆平
日本物理学会誌/75(1)/pp.28-33, 2020-01 - レアイベントサンプリング法の開発と応用研究
原田 隆平; Sladek Vladimir; 重田育照
日本コンピュータ化学会/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 - 分子動力学シミュレーションによる不凍タンパク質RiAFPの氷の結晶成長に及ぼす影響の解析
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 - さらに表示...
- 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