Harada Ryuhei 原田隆平

Researcher Number	60612174
Other IDs
Affiliation (Current)	2025: 筑波大学, 計算科学研究センター, 准教授
Affiliation (based on the past Project Information) *help	2025: 筑波大学, 計算科学研究センター, 准教授 2021 – 2023: 筑波大学, 計算科学研究センター, 准教授 2018: 筑波大学, 計算科学研究センター, 准教授 2016 – 2017: 筑波大学, 計算科学研究センター, 助教 2015: 筑波大学, 数理物質系, 特別研究員 2015: 筑波大学, 数理物質系, 特別研究員(PD) 2014: 筑波大学, 筑波大学計算科学研究センター, 研究員
Review Section/Research Field	Principal Investigator Biophysics / Basic Section 62010:Life, health and medical informatics-related / Basic Section 43040:Biophysics-related Except Principal Investigator Medium-sized Section 39:Agricultural and environmental biology and related fields
Keywords	Principal Investigator タンパク質 / 分子動力学シミュレーション / レアイベント / レアイベントサンプリング / タンパク質の構造変化 / 分子内・分子間コンタクト / タンパク質の効率的な構造探索 / 解離過程 / 異常検知 / 構造探索 … More / 多量体 / 分子間相互作用 / 解離プロセス / 複合体 / 機械学習 / 構造変化 / 分子動力学計算 / 生物物理学 / タンパク質の構造探索 / Gタンパク質共役受容体 / 自由エネルギー地形 / 超並列シミュレーション / 機能発現 / 構造サンプリング / フォールディング / 立体構造変化 / タンパク質の構造変化予測 / タンパク質の天然構造予測 … More Except Principal Investigator 計算科学的解析 / 機能 / 構造 / Rubisco Less

薬効発揮に重要な長時間ダイナミクスを抽出・解析する分子シミュレーション手法の開発Principal Investigator
- Principal Investigator
  
  原田隆平
- Project Period (FY)
  2025 – 2028
- Research Category
  
  Grant-in-Aid for Scientific Research (B)
- Review Section
  
  Basic Section 62010:Life, health and medical informatics-related
- Research Institution
  University of Tsukuba
Identification of structural factors to improve Rubisco
- Principal Investigator
  
  松村浩由
- Project Period (FY)
  2023 – 2025
- Research Category
  
  Grant-in-Aid for Challenging Research (Exploratory)
- Review Section
  
  Medium-sized Section 39:Agricultural and environmental biology and related fields
- Research Institution
  Ritsumeikan University
Prediction of Protein Dynamics Based on a Combination of Molecular Dynamics Simulation and Machine LearningPrincipal Investigator
- Principal Investigator
  
  Harada Ryuhei
- Project Period (FY)
  2021 – 2023
- Research Category
  
  Grant-in-Aid for Scientific Research (C)
- Review Section
  
  Basic Section 43040:Biophysics-related
- Research Institution
  University of Tsukuba
Signal Transduction Process of G-Protein Coupled Receptor (GPCR) Studied by Molecular Dynamics SimulationPrincipal Investigator
- Principal Investigator
  
  HARADA Ryuhei
- Project Period (FY)
  2016 – 2018
- Research Category
  
  Grant-in-Aid for Young Scientists (A)
- Research Field
  
  Biophysics
- Research Institution
  University of Tsukuba
Developments of methods for predicting transitions of proteins based on structural fluctuationsPrincipal Investigator
- Principal Investigator
  
  Harada Ryuhei
- Project Period (FY)
  2014 – 2015
- Research Category
  
  Grant-in-Aid for Young Scientists (B)
- Research Field
  
  Biophysics
- Research Institution
  University of Tsukuba

All 2023 2022 2021 2019 2018 2017 2016 2015 2014 Other

All Journal Article Presentation Patent

[Journal Article] Design of electron-donating group substituted 2-PAM analogs as antidotes for organophosphate insecticide poisoning2023
- Author(s)
  Kongkaew Nalinee、Hengphasatporn Kowit、Injongkol Yuwanda、Mee-udorn Pitchayathida、Shi Liyi、Mahalapbutr Panupong、Maitarad Phornphimon、Harada Ryuhei、Shigeta Yasuteru、Rungrotmongkol Thanyada、Vangnai Alisa S.
- Journal Title
  
  RSC Advances
  
  Volume: 13 Issue: 46 Pages: 32266-32275
- DOI
  10.1039/d3ra03087c
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-21K06094, KAKENHI-PLANNED-21H05269
[Journal Article] Determination of the Association between Mesotrione Sensitivity and Conformational Change of 4-Hydroxyphenylpyruvate Dioxygenase via Free-Energy Analyses2023
- Author(s)
  Yohei Munei, Kowit Hengphasatporn, Yuta Hori, Ryuhei Harada, and Yasuteru Shigeta
- Journal Title
  
  Journal of Agricultural and Food Chemistry
  
  Volume: 71 Issue: 24 Pages: 9528-9537
- DOI
  10.1021/acs.jafc.3c01253
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-21K06094
[Journal Article] Pathological mutations promote proteolysis of mitochondrial tRNA-specific 2-thiouridylase 1 (MTU1) via mitochondrial caseinolytic peptidase (CLPP)2023
- Author(s)
  Ahmad Raja Norazireen?Raja、Zhang Long-Teng、Morita Rikuri、Tani Haruna、Wu Yong、Chujo Takeshi、Ogawa Akiko、Harada Ryuhei、Shigeta Yasuteru、Tomizawa Kazuhito、Wei Fan-Yan
- Journal Title
  
  Nucleic Acids Research
  
  Volume: 52 Issue: 3 Pages: 1341-1358
- DOI
  10.1093/nar/gkad1197
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-23K18088, KAKENHI-PROJECT-23K14113, KAKENHI-PROJECT-23K16989, KAKENHI-PROJECT-21K06094, KAKENHI-PROJECT-22KJ0156, KAKENHI-PUBLICLY-22H04628, KAKENHI-PROJECT-23K21370, KAKENHI-PROJECT-21H02731, KAKENHI-PROJECT-23K24075
[Journal Article] Efficient Screening of Protein-Ligand Complexes in Lipid Bilayers Using LoCoMock Score2023
- Author(s)
  Rikuri Morita, Yasuteru Shigeta, Ryuhei Harada
- Journal Title
  
  Journal of Computer-Aided Molecular Design
  
  Volume: 37 Issue: 4 Pages: 217-225
- DOI
  10.1007/s10822-023-00502-8
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-21K06094
[Journal Article] Free-energy Profiles for Membrane Permeation of Compounds Calculated Using Rare-Event Sampling Methods2023
- Author(s)
  Ryuhei Harada, Rikuri Morita, Yasuteru Shigeta
- Journal Title
  
  Journal of Chemical Information and Modeling
  
  Volume: 63 Issue: 1 Pages: 259-269
- DOI
  10.1021/acs.jcim.2c01097
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-21K06094
[Journal Article] A Structural Refinement Technique for Protein-RNA Complexes Based on a Combination of AI-based Modeling and Flexible Docking: A Study of Musashi-1 Protein2023
- Author(s)
  Darai Nitchakan、Hengphasatporn Kowit、Wolschann Peter、Wolfinger Michael T、Shigeta Yasuteru、Rungrotmongkol Thanyada、Harada Ryuhei
- Journal Title
  
  Bulletin of the Chemical Society of Japan
  
  Volume: 96 Issue: 7 Pages: 677-685
- DOI
  10.1246/bcsj.20230092
- Data Source
  KAKENHI-PROJECT-21K06094
[Journal Article] Latrunculin resistance mechanism of non‐conventional actin NAP1 uncovered by molecular dynamics simulations2023
- Author(s)
  Morita Rikuri、Shigeta Yasuteru、Harada Ryuhei
- Journal Title
  
  Cytoskeleton
  
  Volume: 81 Issue: 2-3 Pages: 143-150
- DOI
  10.1002/cm.21798
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-23K16989, KAKENHI-PROJECT-21K06094
[Journal Article] A Variety of Initial Velocities in Restarting Molecular Dynamics Simulations Promotes Protein Transitions2023
- Author(s)
  Munei Yohei、Shigeta Yasuteru、Harada Ryuhei
- Journal Title
  
  Chemistry Letters
  
  Volume: 52 Issue: 5 Pages: 385-388
- DOI
  10.1246/cl.230104
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-21K06094
[Journal Article] Promising SARS-CoV-2 Main Protease Inhibitor Ligand-Binding Modes Evaluated Using LB-PaCS-MD/FMO2022
- Author(s)
  Kowit Hengphasatporn, Ryuhei Harada, Patcharin Wilasluck, Peerapon Deetanya, Edwin R Sukandar, Warinthorn Chavasiri, Aphinya Suroengrit, Siwaporn Boonyasuppayakorn, Thanyada Rungrotmongkol, Kittikhun Wangkanont, Yasuteru Shigeta
- Journal Title
  
  Scientific Report
  
  Volume: 12 Issue: 1 Pages: 17984-17984
- DOI
  10.1038/s41598-022-22703-1
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-21K06094, KAKENHI-PUBLICLY-22H04800
[Journal Article] Protein Structure Validation Derives a Smart Conformational Search in a Physically Relevant Configurational Subspace2022
- Author(s)
  Takunori Yasuda, Rikuri Morita, Yasuteru Shigeta, Ryuhei Harada
- Journal Title
  
  Journal of Chemical Information and Modeling
  
  Volume: 62 Issue: 23 Pages: 6217-6227
- DOI
  10.1021/acs.jcim.2c01173
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-21K06094, KAKENHI-PROJECT-22KJ0421
[Journal Article] Autism-Associated Mutation in Hevin Induces Endoplasmic Reticulum Stress Through Structural Instability2022
- Author(s)
  Takumi Taketomi, Takunori Yasuda, Rikuri Morita, Jaehyun Kim, Yasuteru Shigeta, Cagla Eroglu, Ryuhei Harada, Fuminori Tsuruta
- Journal Title
  
  Scientific Report
  
  Volume: 12 Issue: 1 Pages: 11891-11891
- DOI
  10.1038/s41598-022-15784-5
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-21K06094, KAKENHI-PROJECT-22KJ0421, KAKENHI-PROJECT-20K05951
[Journal Article] The Structural Validation by G-factor Regulates Boost Potentials Employed in Conformational Sampling of Proteins2022
- Author(s)
  Takunori Yasuda, Rikuri Morita, Yasuteru Shigeta, Ryuhei Harada
- Journal Title
  
  Journal of Chemical Information and Modeling
  
  Volume: 62 Issue: 14 Pages: 3442-3452
- DOI
  10.1021/acs.jcim.2c00573
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-21K06094, KAKENHI-PROJECT-22KJ0421
[Journal Article] The Role of ATP in Solubilizing RNA-binding Protein Fused in Sarcoma2022
- Author(s)
  Hayato Aida, Yasuteru Shigeta, Ryuhei Harada
- Journal Title
  
  Proteins: Structure, Function, and Bioinformatics
  
  Volume: 90 Issue: 8 Pages: 1606-1612
- DOI
  10.1002/prot.26335
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-21K06094
[Journal Article] Split conformation of Chaetomium thermophilum Hsp104 disaggregase2021
- Author(s)
  Inoue Yosuke、Hanazono Yuya、Noi Kentaro、Kawamoto Akihiro、Kimatsuka Masato、Harada Ryuhei、Takeda Kazuki、Kita Ryoichi、Iwamasa Natsuki、Shibata Kyoka、Noguchi Keiichi、Shigeta Yasuteru、Namba Keiichi、Ogura Teru、Miki Kunio、Shinohara Kyosuke、Yohda Masafumi
- Journal Title
  
  Structure
  
  Volume: － Issue: 7 Pages: 1-10
- DOI
  10.1016/j.str.2021.02.002
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PUBLICLY-20H05497, KAKENHI-PROJECT-21K06094
[Journal Article] A Post-Process to Estimate an Approximated Minimal Free Energy Path Based on Local Centroids2021
- Author(s)
  Rikuri Morita, Yasuteru Shigeta, Ryuhei Harada
- Journal Title
  
  Chemical Physics Letters
  
  Volume: 782 Pages: 139003-139003
- DOI
  10.1016/j.cplett.2021.139003
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-21K06094
[Journal Article] Independent Nontargeted Parallel Cascade Selection Molecular Dynamics (Ino-PaCS-MD) to Enhance the Conformational Sampling of Proteins2021
- Author(s)
  Yasuda Takunori、Morita Rikuri、Shigeta Yasuteru、Harada Ryuhei
- Journal Title
  
  Journal of Chemical Theory and Computation
  
  Volume: 17 Issue: 9 Pages: 5933-5943
- DOI
  10.1021/acs.jctc.1c00558
- Peer Reviewed
- Data Source
  KAKENHI-PUBLICLY-20H05497, KAKENHI-PROJECT-21K06094
[Journal Article] Solubility and Membrane Permeability of Cyclic Dipeptides Approximately Estimated by Quantum Chemistry and Molecular Dynamics Calculations2021
- Author(s)
  Yanagi Koki、Mitsuta Yuki、Takaoka Kenta、Takahashi Teruyuki、Hengphasatporn Kowit、Harada Ryuhei、Shigeta Yasuteru
- Journal Title
  
  Chemistry Letters
  
  Volume: 50 Issue: 12 Pages: 1964-1967
- DOI
  10.1246/cl.210488
- NAID
  130008131925
- Peer Reviewed
- Data Source
  KAKENHI-PUBLICLY-20H05497, KAKENHI-PROJECT-21K06094
[Journal Article] Residue Folding Degree - Relationship to Secondary Structure Categories and use as Collective Variable2021
- Author(s)
  Vladimir Sladek, Ryuhei Harada, Yasuteru Shigeta
- Journal Title
  
  International Journal of Molecular Sciences
  
  Volume: 22 Issue: 23 Pages: 13042-13042
- DOI
  10.3390/ijms222313042
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-21K06094
[Journal Article] In Silico Mutational Analyses Reveal Different Ligand-Binding Abilities of Double Pockets of Medaka Fish Taste Receptor Type 1 Essential for Efficient Taste Recognitions2021
- Author(s)
  Hayato Aida, Rikuri Morita, Yasuteru Shigeta, Ryuhei Harada
- Journal Title
  
  Physical Chemistry Chemical Physics
  
  Volume: 23 Issue: 36 Pages: 20398-20405
- DOI
  10.1039/d1cp02876f
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-21K06094
[Journal Article] Comprehensive predictions of secondary structures for comparative analysis in different species2021
- Author(s)
  Morita Rikuri、Shigeta Yasuteru、Harada Ryuhei
- Journal Title
  
  Journal of Structural Biology
  
  Volume: 213 Issue: 2 Pages: 107735-107735
- DOI
  10.1016/j.jsb.2021.107735
- Peer Reviewed
- Data Source
  KAKENHI-PUBLICLY-20H05497, KAKENHI-PROJECT-21K06094
[Journal Article] Structural Variations of Metallothionein with or without Zinc Ions Elucidated by All-Atom Molecular Dynamics Simulations2021
- Author(s)
  Morita Rikuri、Shigeta Yasuteru、Harada Ryuhei
- Journal Title
  
  The Journal of Physical Chemistry B
  
  Volume: 125 Issue: 46 Pages: 12712-12717
- DOI
  10.1021/acs.jpcb.1c07928
- Peer Reviewed
- Data Source
  KAKENHI-PUBLICLY-20H05497, KAKENHI-PROJECT-21K06094
[Journal Article] pyProGA - A PyMOL Plugin for Protein Residue Network Analysis2021
- Author(s)
  Vladimir Sladek, Yuta Yamamoto, Ryuhei Harada, Mitsuo Shoji, Yasuteru Shigeta
- Journal Title
  
  PLoS ONE
  
  Volume: 16
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-21K06094
[Journal Article] Hybrid Cascade-Type Molecular Dynamics with a Markov State Model for Efficient Free Energy Calculations2019
- Author(s)
  Ryuhei Harada, Yasuteru Shigeta
- Journal Title
  
  Journal of Chemical Theory and Computation
  
  Volume: 15 Issue: 1 Pages: 680-687
- DOI
  10.1021/acs.jctc.8b00802
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-16H06164
[Journal Article] Possible Configurations of Apo-form Taste Receptor Type 1 (T1r) Studied by Microsecond-order Molecular Dynamics Simulation2019
- Author(s)
  Hayato Aida, Ryuhei, Harada, Yasuteru Shigeta
- Journal Title
  
  Chemistry Letters
  
  Volume: 48 Issue: 4 Pages: 325-328
- DOI
  10.1246/cl.181030
- NAID
  130007624447
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-16H06164
[Journal Article] Effects of Antifreezing Protein from Rhagium inquisitor Binding on Ice Growth: A Molecular Dynamics Study2019
- Author(s)
  Kimatsuka Masato, Ryuma Sato, Ryuhei Harada, Mitsuo Shoji, Yasuteru Shigeta
- Journal Title
  
  Chemistry Letters
  
  Volume: 17 Issue: 3 Pages: 222-224
- DOI
  10.1246/cl.180963
- NAID
  130007607565
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-16H06164
[Journal Article] Temperature-pressure shuffling outlier flooding method enhances the conformational sampling of proteins2019
- Author(s)
  Harada Ryuhei、Yoshino Ryunosuke、Nishizawa Hiroaki、Shigeta Yasuteru
- Journal Title
  
  Journal of Computational Chemistry
  
  Volume: 40 Issue: 15 Pages: 1530-1537
- DOI
  10.1002/jcc.25806
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-18K18150, KAKENHI-PROJECT-16H06164
[Journal Article] Parallel Cascade Selection Molecular Dynamics Simulations for Transition Pathway Sampling of Biomolecules2019
- Author(s)
  Ryuhei Harada, Yasuteru Shigeta
- Journal Title
  
  Advances in Quantum Chemistry
  
  Volume: 78 Pages: 129-147
- DOI
  10.1016/bs.aiq.2018.05.002
- ISBN
  9780128160848
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-16H06164
[Journal Article] Selection rules on initial structures in parallel cascade selection molecular dynamics affect conformational sampling efficiency2018
- Author(s)
  Ryuhei Harada, Yasuteru Shigeta
- Journal Title
  
  Journal of Molecular Graphics and Modelling
  
  Volume: 85 Pages: 153-159
- DOI
  10.1016/j.jmgm.2018.08.014
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-16H06164
[Journal Article] How low-resolution structural data predict the conformational changes of a protein: a study on data-driven molecular dynamics simulations2018
- Author(s)
  Ryuhei Harada, Yasuteru Shigeta
- Journal Title
  
  Physical Chemistry Chemical Physics
  
  Volume: 20 Issue: 26 Pages: 17790-17798
- DOI
  10.1039/c8cp02246a
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-16H06164
[Journal Article] Simple, yet Efficient Conformational Sampling Methods for Reproducing/Predicting Biologically Rare Events of Proteins2018
- Author(s)
  Ryuhei Harada
- Journal Title
  
  Bulletin of the Chemical Society of Japan
  
  Volume: 91 Issue: 9 Pages: 1436-1450
- DOI
  10.1246/bcsj.20180170
- NAID
  130007484183
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-16H06164
[Journal Article] Programed dynamical ordering in self-organization processes of a nanocube: a molecular dynamics study2018
- Author(s)
  Harada Ryuhei、Mashiko Takako、Tachikawa Masanori、Hiraoka Shuichi、Shigeta Yasuteru
- Journal Title
  
  Physical Chemistry Chemical Physics
  
  Volume: 20 Issue: 14 Pages: 9115-9122
- DOI
  10.1039/c8cp00284c
- Peer Reviewed
- Data Source
  KAKENHI-PUBLICLY-16H00780, KAKENHI-ORGANIZER-25102001, KAKENHI-PLANNED-25102005, KAKENHI-PROJECT-15J03797, KAKENHI-PROJECT-18H01945, KAKENHI-PROJECT-16H06164, KAKENHI-PROJECT-15KT0067
[Journal Article] Coulomb and CH-π interactions in (6-4) photolyase-DNA complex dominate DNA binding and repair abilities2018
- Author(s)
  Terai Yuma、Sato Ryuma、Yumiba Takahiro、Harada Ryuhei、Shimizu Kohei、Toga Tatsuya、Ishikawa-Fujiwara Tomoko、Todo Takeshi、Iwai Shigenori、Shigeta Yasuteru、Yamamoto Junpei
- Journal Title
  
  Nucleic Acids Research
  
  Volume: 46 Issue: 13 Pages: 6761-6772
- DOI
  10.1093/nar/gky364
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-18K19476, KAKENHI-PLANNED-26107004, KAKENHI-PROJECT-15H05713, KAKENHI-PROJECT-16H06164, KAKENHI-PROJECT-16K07321
[Journal Article] On-the-Fly Specifications of Reaction Coordinates in Parallel Cascade Selection Molecular Dynamics Accelerate Conformational Transitions of Proteins2018
- Author(s)
  Ryuhei Harada, Yasuteru Shigeta
- Journal Title
  
  Journal of Chemical Theory and Computation
  
  Volume: 14 Issue: 6 Pages: 3332-3341
- DOI
  10.1021/acs.jctc.8b00264
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-16H06164
[Journal Article] Temperature-Shuffled Structural Dissimilarity Sampling Based on a Root-Mean-Square Deviation2018
- Author(s)
  Ryuhei Harada, Yasuteru Shigeta
- Journal Title
  
  Journal of Chemical Information and Modeling
  
  Volume: 58 Issue: 7 Pages: 1397-1405
- DOI
  10.1021/acs.jcim.8b00095
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-16H06164
[Journal Article] How Does Friction Coefficient Affect the Conformational Sampling Efficiency of Parallel Cascade Selection Molecular Dynamics?2018
- Author(s)
  Ryuhei Harada, Yasuteru Shigeta
- Journal Title
  
  Chemistry Letters
  
  Volume: 47 Issue: 9 Pages: 1119-1122
- DOI
  10.1246/cl.180464
- NAID
  130007472092
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-16H06164
[Journal Article] The Formation of Hydrophobic Core Regulates the Protein Folding of Villin Elucidated with Parallel Cascade Selection Molecular Dynamics2018
- Author(s)
  Ryuhei Harada, Hayato Aida, Yasuteru Shigeta
- Journal Title
  
  Chemistry Letters
  
  Volume: 47 Issue: 10 Pages: 1300-1303
- DOI
  10.1246/cl.180596
- NAID
  130007495956
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-16H06164
[Journal Article] Self-Avoiding Conformational Sampling (SACS) Based on Histories of Past Conformational Searches2017
- Author(s)
  *R. Harada, *Y. Shigeta
- Journal Title
  
  Journal of Chemical Information and Modeling
  
  Volume: 57 Issue: 12 Pages: 3070-3078
- DOI
  10.1021/acs.jcim.7b00573
- Peer Reviewed
- Data Source
  KAKENHI-PLANNED-26105012, KAKENHI-PROJECT-16H06164, KAKENHI-PROJECT-15J03797
[Journal Article] Dynamic Specification of Initial Structures in Parallel Cascade Selection Molecular Dynamics (PaCS-MD) Efficiently Promotes Biologically Relevant Rare Events2017
- Author(s)
  Harada Ryuhei、Shigeta Yasuteru
- Journal Title
  
  Bulletin of the Chemical Society of Japan
  
  Volume: 90 Issue: 11 Pages: 1236-1243
- DOI
  10.1246/bcsj.20170177
- NAID
  130006201499
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-INTERNATIONAL-15K21719, KAKENHI-PLANNED-26105012, KAKENHI-PROJECT-16H06164, KAKENHI-PROJECT-15J03797
[Journal Article] Classical cumulant dynamics for statistical chemical physics2017
- Author(s)
  Yasuteru Shigeta, Ryuhei Harada, Ryuma Sato, Hirotaka Kitoh-Nishioka, My Bui Thi Kieu, Akimasa Sato, Takaki Tokiwa, Akane Kyan, Yuki Ishii, Masato Kimatsuka, Sotaro Yamasaki, Megumi Kayanuma, Mitsuo Shoji
- Journal Title
  
  Molecular Simulation
  
  Volume: 43 Issue: 13-16 Pages: 1260-1268
- DOI
  10.1080/08927022.2017.1315770
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-16H06164
[Journal Article] How does the number of initial structures affect the conformational sampling efficiency and quality in parallel cascade selection molecular dynamics (PaCS-MD)?2017
- Author(s)
  Ryuhei Harada, Yasuteru Shigeta
- Journal Title
  
  Chemistry Letters
  
  Volume: 47 Issue: 6 Pages: 862-865
- DOI
  10.1246/cl.170207
- NAID
  130005689326
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-16H06164, KAKENHI-PROJECT-15J03797
[Journal Article] Molecular Mechanism of the Reaction Specificity in Threonine Synthase: Importance of the Substrate Conformations2017
- Author(s)
  Ujiie Yuzuru，Tanaka Wataru，Hanaoka Kyohei，Harada Ryuhei，Kayanuma Megumi，Shoji Mitsuo，Murakawa Takeshi，Ishida Toyokazu，Shigeta Yasuteru，Hayashi Hideyuki
- Journal Title
  
  The Journal of Physical Chemistry B
  
  Volume: 121 Issue: 22 Pages: 5536-5543
- DOI
  10.1021/acs.jpcb.7b02932
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-15K05573, KAKENHI-PROJECT-16H06164, KAKENHI-PROJECT-15J03797
[Journal Article] Structural dissimilarity sampling with dynamically self-guiding selection2017
- Author(s)
  Harada Ryuhei、Shigeta Yasuteru
- Journal Title
  
  Journal of Computational Chemistry
  
  Volume: 38 Issue: 22 Pages: 1921-1929
- DOI
  10.1002/jcc.24837
- Peer Reviewed
- Data Source
  KAKENHI-INTERNATIONAL-15K21719, KAKENHI-PLANNED-26105012, KAKENHI-PROJECT-16H06164, KAKENHI-PROJECT-15J03797
[Journal Article] Identification of the key interactions in structural transition pathway of FtsZ from Staphylococcus aureus2017
- Author(s)
  J. Fujita, R. Harada, Y. Maeda, Y. Saito, E. Mizohata, T. Inoue, Y. Shigeta, H. Matsumura
- Journal Title
  
  J. Struct. Biol.
  
  Volume: 198 Issue: 2 Pages: 65-73
- DOI
  10.1016/j.jsb.2017.04.008
- Peer Reviewed / Acknowledgement Compliant
- Data Source
  KAKENHI-PUBLICLY-16H00783, KAKENHI-PUBLICLY-17H05732, KAKENHI-PROJECT-16H06164, KAKENHI-PROJECT-15J00589, KAKENHI-PROJECT-15J03797
[Journal Article] Temperature-shuffled parallel cascade selection molecular dynamics accelerates the structural transitions of proteins2017
- Author(s)
  Harada Ryuhei、Shigeta Yasuteru
- Journal Title
  
  Journal of Computational Chemistry
  
  Volume: 38 Issue: 31 Pages: 2671-2674
- DOI
  10.1002/jcc.25060
- Peer Reviewed
- Data Source
  KAKENHI-INTERNATIONAL-15K21719, KAKENHI-ORGANIZER-26105001, KAKENHI-PLANNED-26105012, KAKENHI-PLANNED-26107004, KAKENHI-PROJECT-16H06164, KAKENHI-PROJECT-15J03797
[Journal Article] Efficient conformational search based on Structural Dissimilarity Sampling: Applications to reproductions of structural transitions on Maltodextrin Binding Protein2017
- Author(s)
  R. Harada, Y. Shigeta
- Journal Title
  
  J. Chem. Theoret. Comp.
  
  Volume: 13 Issue: 3 Pages: 1411-1423
- DOI
  10.1021/acs.jctc.6b01112
- Peer Reviewed / Acknowledgement Compliant / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-26107004, KAKENHI-PROJECT-15J03797, KAKENHI-PROJECT-16H06164
[Journal Article] 最近の研究から「カスケード型超並列シミュレーションに基づく遷移経路探索法」2016
- Author(s)
  原田隆平
- Journal Title
  
  Ensemble
  
  Volume: 18 Issue: 3 Pages: 159-167
- DOI
  10.11436/mssj.18.159
- NAID
  130005874978
- ISSN
  1884-5088, 1884-6750
- Language
  Japanese
- Data Source
  KAKENHI-PROJECT-16H06164
[Journal Article] Theoretical analyses on a flipping mechanism of UV-induced DNA damage2016
- Author(s)
  R. Sato, R. Harada, Y. Shigeta
- Journal Title
  
  Biophys. Physicobio.
  
  Volume: 13 Issue: 0 Pages: 311-319
- DOI
  10.2142/biophysico.13.0_311
- NAID
  130005433879
- Peer Reviewed / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-26107004, KAKENHI-PROJECT-15J03797, KAKENHI-PROJECT-16H06164
[Journal Article] Sparsity-weighted Outlier FLOODing (OFLOOD) method: Efficient rare event sampling method using sparsity of distribution2016
- Author(s)
  R. Harada, T. Nakamura, Y. Shigeta
- Journal Title
  
  J. Comp. Chem.
  
  Volume: 37 Issue: 8 Pages: 724-728
- DOI
  10.1002/jcc.24255
- Peer Reviewed / Acknowledgement Compliant / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-26107004, KAKENHI-PROJECT-15J03797, KAKENHI-PROJECT-16H06164
[Journal Article] A Fast Convergent Simulated Annealing Algorithm: Simulated Annealing Outlier FLOODing (SA-OFLOOD) Method2016
- Author(s)
  R. Harada, T. Nakamura, Y. Shigeta
- Journal Title
  
  Bull. Chem. Soc. Jpn.
  
  Volume: 89 Issue: 11 Pages: 1361-1367
- DOI
  10.1246/bcsj.20160244
- NAID
  130005316155
- Peer Reviewed / Acknowledgement Compliant / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-26107004, KAKENHI-PROJECT-15J03797, KAKENHI-PROJECT-16H06164
[Journal Article] Biomolecular interactions modulate macromolecular structure and dynamics in atomistic model of a bacterial cytoplasm2016
- Author(s)
  Yu I, Mori T, Ando T, Harada R, Jung J, Sugita Y, Feig M
- Journal Title
  
  eLife
  
  Volume: 5
- DOI
  10.7554/elife.19274
- Peer Reviewed / Acknowledgement Compliant / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-26119006, KAKENHI-PROJECT-15J03797, KAKENHI-PROJECT-25410025, KAKENHI-PROJECT-16H06164
[Journal Article] Common folding processes of the fast-folding proteins: Partial formations of secondary structures initiate the immediate protein folding2016
- Author(s)
  *R. Harada,*Y. Takano, *Y. Shigeta,
- Journal Title
  
  J. Comput. Chem. in press.
  
  Volume: - Issue: 11 Pages: 767-853
- DOI
  10.1002/jcc.24748
- Peer Reviewed / Acknowledgement Compliant / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-ORGANIZER-26105001, KAKENHI-PLANNED-26105012, KAKENHI-PROJECT-15J03797, KAKENHI-INTERNATIONAL-15K21719, KAKENHI-PROJECT-16H06164
[Journal Article] Molecular mechanisms of substrate specificities of uridine-cytidine kinase2016
- Author(s)
  W. Tanaka, M. Shoji, F. Tomoike, Y. Ujiie, K. Hanaoka, R. Harada, M. Kayanuma, K. Kamiya, T. Ishida, R. Masui, S. Kuramitsu, Y. Shigeta
- Journal Title
  
  Biophysics and Physicobiology
  
  Volume: 13 Issue: 0 Pages: 77-84
- DOI
  10.2142/biophysico.13.0_77
- NAID
  130005156955
- ISSN
  2189-4779
- Language
  English
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-26410002, KAKENHI-PROJECT-15K21459, KAKENHI-PROJECT-24000018, KAKENHI-PROJECT-16H06164
[Journal Article] TaBoo SeArch (TBSA) algorithm with a modified inverse histogram for reproducing biologically relevant rare-events of proteins,2016
- Author(s)
  *R. Harada,*Y. Takano, *Y. Shigeta,
- Journal Title
  
  J. Chem. Theory Comput.,
  
  Volume: 12 Issue: 5 Pages: 2346-2445
- DOI
  10.1021/acs.jctc.6b00082
- Peer Reviewed / Acknowledgement Compliant / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-ORGANIZER-26105001, KAKENHI-PLANNED-26105012, KAKENHI-PROJECT-15J03797, KAKENHI-INTERNATIONAL-15K21719, KAKENHI-PROJECT-16H06164
[Journal Article] Parallel cascade selection molecular dynamics for efficient conformational sampling and free energy calculation of proteins2016
- Author(s)
  Akio Kitao, Ryuhei Harada, Yasutaka Nishihara, Duy Phuoc Tran
- Journal Title
  
  AIP Conference Proceedings
  
  Volume: 1790
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-16H06164
[Journal Article] Efficient conformational sampling of proteins based on a multi-dimensional TaBoo SeArch algorithm:2015
- Author(s)
  Ryuhei Harada, Yu Takano, Yasuteru Shigeta
- Journal Title
  
  Chemical Physics Letters
  
  Volume: 630 Pages: 68-75
- DOI
  10.1016/j.cplett.2015.04.039
- Peer Reviewed / Acknowledgement Compliant
- Data Source
  KAKENHI-ORGANIZER-26105001, KAKENHI-PLANNED-26105012, KAKENHI-PROJECT-15J03797, KAKENHI-PROJECT-26840056
[Journal Article] Automatic Detection of Hidden Dimension in OFLOOD Method2015
- Author(s)
  Ryuhei Harada, Tomotake Nakamura, Yasuteru Shigeta
- Journal Title
  
  Chemical Physics Letters
  
  Volume: 639 Pages: 269-274
- DOI
  10.1016/j.cplett.2015.09.031
- Peer Reviewed / Acknowledgement Compliant
- Data Source
  KAKENHI-PROJECT-15J03797, KAKENHI-PROJECT-26840056, KAKENHI-PLANNED-26107004
[Journal Article] Simple, yet powerful methodologies for conformational sampling of proteins2015
- Author(s)
  Ryuhei Harada, Yu Takano, Takeshi Baba, Yasuteru Shigeta
- Journal Title
  
  Physical Chemistry Chemical Physics
  
  Volume: 17 Issue: 9 Pages: 6155-6173
- DOI
  10.1039/c4cp05262e
- Peer Reviewed / Acknowledgement Compliant
- Data Source
  KAKENHI-PLANNED-26105012, KAKENHI-PLANNED-26107004, KAKENHI-PROJECT-15J03797, KAKENHI-PROJECT-26840056
[Journal Article] Enhanced conformational sampling method for proteins based on the TaBoo SeArch (TBSA) algorithm: Application to the folding of a mini-protein, chignolin2015
- Author(s)
  Ryuhei Harada, Yu Takano, Yasuteru Shigeta
- Journal Title
  
  Journal of Computational Chemistry
  
  Volume: 36 Issue: 10 Pages: 763-772
- DOI
  10.1002/jcc.23854
- Peer Reviewed / Acknowledgement Compliant
- Data Source
  KAKENHI-PLANNED-26105012, KAKENHI-PROJECT-15J03797, KAKENHI-PROJECT-26840056, KAKENHI-PLANNED-26107004
[Journal Article] Non-targeted parallel cascade selection molecular dynamics (nt-PaCS-MD) for enhancement of the conformational sampling of proteins2015
- Author(s)
  Ryuhei Harada and Akio Kitao
- Journal Title
  
  J. Chem. Theor. Comput.
  
  Volume: 11 Issue: 11 Pages: 5493-5502
- DOI
  10.1021/acs.jctc.5b00723
- Peer Reviewed / Acknowledgement Compliant / Open Access
- Data Source
  KAKENHI-PLANNED-25104002, KAKENHI-PROJECT-15H04357, KAKENHI-PROJECT-15J03797, KAKENHI-PROJECT-26840056
[Journal Article] Complete Atomistic Model of a Bacterial Cytoplasm for Integrating Physics, Biochemistry, and Systems Biology2015
- Author(s)
  Michael Feig, Ryuhei Harada, Takaharu Mori, Isseki Yu, Koich Takahashi, Yuji Sugita
- Journal Title
  
  Jornal of Molecular Graphics and Modelling
  
  Volume: 56 Pages: 1-9
- DOI
  10.1016/j.jmgm.2015.02.004
- Peer Reviewed / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-15J03797, KAKENHI-PROJECT-26840056
[Journal Article] Protein folding pathways extracted by OFLOOD: Outlier FLOODing method2015
- Author(s)
  Ryuhei Harada, Tomotake Nakamura, Yu Takano, Yasuteru Shigeta
- Journal Title
  
  Journal of Computational Chemistry
  
  Volume: 36 Issue: 2 Pages: 97-102
- DOI
  10.1002/jcc.23773
- Peer Reviewed / Acknowledgement Compliant
- Data Source
  KAKENHI-PLANNED-26105012, KAKENHI-PLANNED-26107004, KAKENHI-PROJECT-15J03797, KAKENHI-PROJECT-26840056
[Journal Article] Quantal cumulant dynamics for real-time simulations of quantum many-body systems2015
- Author(s)
  Y. Shigeta, H. Harada, M. Kayanuma, M. Shoji
- Journal Title
  
  Int. J. Quantum Chem.
  
  Volume: 115 Issue: 5 Pages: 300-308
- DOI
  10.1002/qua.24820
- Peer Reviewed / Acknowledgement Compliant
- Data Source
  KAKENHI-PLANNED-26107004, KAKENHI-PROJECT-15J03797, KAKENHI-PROJECT-26840056
[Journal Article] カスケード型超並列シミュレーションによるタンパク質構造遷移のパスウェイ探索2014
- Author(s)
  西原泰孝, 原田隆平, 北尾彰朗
- Journal Title
  
  統計数理
  
  Volume: 62 Pages: 273-284
- NAID
  120006020818
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-26840056
[Journal Article] Conformational transition pathway and free energy analyses of proteins by parallel cascade selection molecular dynamics (PaCS-MD)2014
- Author(s)
  Ryuhei Harada, Yasutaka Nishihara, Nobuhiko Wakai, and Akio Kitao
- Journal Title
  
  AIP Conference Proceedings
  
  Volume: 1618 Pages: 86-86
- DOI
  10.1063/1.4897682
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-23370066, KAKENHI-PLANNED-25104002, KAKENHI-PROJECT-26840056
[Journal Article] Fluctuation Flooding Method (FFM) for accelerating conformational transitions on proteins.2014
- Author(s)
  Ryuhei Harada, Yu Takano, Yasuteru Shigeta
- Journal Title
  
  J. Chem. Phys.
  
  Volume: 140 Issue: 12 Pages: 125103-125103
- DOI
  10.1063/1.4869594
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-23657103, KAKENHI-PUBLICLY-25104717, KAKENHI-PUBLICLY-26102525, KAKENHI-PROJECT-26840056
[Journal Article] Molecular Simulation Methods to Enhance Soft Protein Motions2014
- Author(s)
  原田隆平,北尾彰朗
- Journal Title
  
  Seibutsu Butsuri
  
  Volume: 54 Issue: 3 Pages: 167-171
- DOI
  10.2142/biophys.54.167
- NAID
  130004719369
- ISSN
  0582-4052, 1347-4219
- Language
  Japanese
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-23370066, KAKENHI-PLANNED-25104002, KAKENHI-PROJECT-26840056
[Journal Article] On the induced-fitmechanism of substrate-enzyme binding structures of Nylon-oligomerhydrolase2014
- Author(s)
  T. Baba, R. Harada, M. Nakano, Y. Shigeta
- Journal Title
  
  Journal of Computational Chemistry
  
  Volume: 35 Issue: 16 Pages: 1240-1247
- DOI
  10.1002/jcc.23614
- Peer Reviewed
- Data Source
  KAKENHI-PUBLICLY-26102525, KAKENHI-PROJECT-26840056
[Patent] 情報処理装置, 指標次元抽出方法, および指標次元抽出プログラム2015
- Inventor(s)
  中村朋健, 重田育照, 原田隆平
- Industrial Property Rights Holder
  中村朋健, 重田育照, 原田隆平
- Industrial Property Rights Type
  特許
- Filing Date
  2015-08-07
- Data Source
  KAKENHI-PROJECT-26840056
[Patent] 情報処理装置, シミュレーション手法, およびシミュレーションプログラム2015
- Inventor(s)
  中村朋健, 重田育照, 原田隆平
- Industrial Property Rights Holder
  中村朋健, 重田育照, 原田隆平
- Industrial Property Rights Type
  特許
- Filing Date
  2015-08-07
- Data Source
  KAKENHI-PROJECT-26840056
[Presentation] Integrated AI-based Modeling and Flexible Docking for Protein-RNA Complexes Refinement2023
- Author(s)
  Kowit Hengphasatporn, Yasuteru Shigeta, Ryuhei Harada
- Organizer
  The 61st Annual Meeting of the Biophysical Society of Japan
- Data Source
  KAKENHI-PROJECT-21K06094
[Presentation] Investigating the Binding Pathway of 2-Pralidoxime for Reactivating Organophosphate-Inhibited Human Acetylcholinesterase2023
- Author(s)
  Nalinee Kongkaew, Kowit Hengphasatporn, Yasuteru Shigeta, Thanyada Rungrotmongkol, Ryuhei Harada
- Organizer
  The 6th International Conference on Molecular Simulation
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-21K06094
[Presentation] 生体機能を紐解く分子シミュレーション手法の開発と応用2023
- Author(s)
  原田隆平
- Organizer
  自然科学研究機構計算科学研究センタースーパーコンピュータワークショップ
- Invited
- Data Source
  KAKENHI-PROJECT-21K06094
[Presentation] 次世代インシリコ創薬を開拓する新しい分子シミュレーション手法の開発2023
- Author(s)
  原田隆平
- Organizer
  CBI研究機構量子構造生命科学研究所シンポジウム
- Invited
- Data Source
  KAKENHI-PROJECT-21K06094
[Presentation] 中分子創薬を革新する分子シミュレーション手法の開発2023
- Author(s)
  原田隆平
- Organizer
  第453回 CBI学会講演会
- Invited
- Data Source
  KAKENHI-PROJECT-21K06094
[Presentation] 化合物の結合と膜透過プロセスを紐解くレアイベントサンプリング法の開発2023
- Author(s)
  原田隆平, 森田陸離, Kowit Hengphasatporn, 重田育照
- Organizer
  化合物の結合と膜透過プロセスを紐解くレアイベントサンプリング法の開発
- Data Source
  KAKENHI-PROJECT-21K06094
[Presentation] Parallel Cascade Selection Molecular Dynamics for Sampling Rare Events of Proteins2023
- Author(s)
  Ryuhei Harada
- Organizer
  The 26th International Annual Symposium on Computational Science and Engineering (ANSCSE 26)
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-21K06094
[Presentation] 脂質二重膜を考慮した膜タンパク質に対するドッキング手法の開発2022
- Author(s)
  森田陸離, 重田育照, 原田隆平
- Organizer
  第50回構造活性相関シンポジウム
- Data Source
  KAKENHI-PROJECT-21K06094
[Presentation] タンパク質の機能を解明する分子シミュレーション手法の開発2022
- Author(s)
  原田隆平
- Organizer
  第22回日本蛋白質科学会年会
- Invited
- Data Source
  KAKENHI-PROJECT-21K06094
[Presentation] 生体機能を解明する分子シミュレーション手法の開発と応用2022
- Author(s)
  原田隆平
- Organizer
  物性研短期研究会「理論タンパク質物性科学の最前線：理論と実験との密な協働」
- Invited
- Data Source
  KAKENHI-PROJECT-21K06094
[Presentation] Structural Validation by the G-factor Properly Regulates Boost Potentials Imposed in Conformational Sampling of Proteins2022
- Author(s)
  Takunori Yasuda, Rikuri Morita, Yasuteru Shigeta, Ryuhei Harada
- Organizer
  The 60th Annual Meeting of the Biophysical Society of Japan
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-21K06094
[Presentation] LogP-corrected Membrane Docking Score Screens Protein-Ligand-Membrane Complexes2022
- Author(s)
  Rikuri Morita, Yasuteru Shigeta, Ryuhei Harada
- Organizer
  The 60th Annual Meeting of the Biophysical Society of Japan
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-21K06094
[Presentation] 化合物の膜透過プロセスを紐解く自由エネルギー計算手法の開発2022
- Author(s)
  原田隆平, 森田陸離, 重田育照
- Organizer
  第50回構造活性相関シンポジウム
- Data Source
  KAKENHI-PROJECT-21K06094
[Presentation] 計算科学で紐解く相分離生物学2022
- Author(s)
  原田隆平
- Organizer
  公益社団法人高分子学会関東支部主催「相分離生物学と高分子科学の接点」
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-21K06094
[Presentation] A Computational Study on the Half-Site Activity Mechanism of Homodimeric Tyrosyl tRNA Synthetase2022
- Author(s)
  Yoshino Okamoto, Takunori Yasuda, Rikuri Morita, Yasuteru Shigeta, Ryuhei Harada
- Organizer
  The 60th Annual Meeting of the Biophysical Society of Japan
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-21K06094
[Presentation] Enhanced Samplingにおける構造妥当性の評価は外部バイアスを適切に制御する2022
- Author(s)
  保田拓範, 森田陸離, 重田育照, 原田隆平
- Organizer
  第36回分子シミュレーション討論会
- Data Source
  KAKENHI-PROJECT-21K06094
[Presentation] Molecular Dynamics Simulation Reveals Structural Variations of Metallothionein with or without Zinc Ions2022
- Author(s)
  Rikuri Morita, Yasuteru Shigeta, Ryuhei Harada
- Organizer
  The 8th International Symposium on Metallomics
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-21K06094
[Presentation] 分子動力学計算に基づくシロイヌナズナおよびエンバクHPPD-メソトリオン複合体の結合挙動解析2022
- Author(s)
  宗井陽平, 堀優太, Kowit Hengphasatporn, 原田隆平, 重田育照
- Organizer
  日本コンピューター化学会 2022年秋季年会
- Data Source
  KAKENHI-PROJECT-21K06094
[Presentation] 分子動力学計算で解明する維持メチル化酵素 DNMT1の活性化メカニズム2021
- Author(s)
  保田拓範, 森田陸離, 重田育照, 原田隆平
- Organizer
  第21回日本蛋白質科学会年会
- Data Source
  KAKENHI-PROJECT-21K06094
[Presentation] Classification of Intrinsically Disordered Regions involved in Liquid-Liquid Phase Separation Using the Novel Score2021
- Author(s)
  Hayato Aida, Ryuhei Harada, Yasuteru Shigeta, Kentaro Tomii
- Organizer
  第59回日本生物物理学会
- Data Source
  KAKENHI-PROJECT-21K06094
[Presentation] ペプチドの膜透過性を評価する分子シミュレーション技術の創出2021
- Author(s)
  原田隆平
- Organizer
  CBI学会（情報計算化学生物学会）2021年度大会フォーカストセッション「ペプチド創薬を指向した計算科学の最前線」
- Data Source
  KAKENHI-PROJECT-21K06094
[Presentation] タンパク質二次構造の網羅的予測2021
- Author(s)
  森田陸離, 重田育照, 原田隆平
- Organizer
  第21回日本蛋白質科学会年会
- Data Source
  KAKENHI-PROJECT-21K06094
[Presentation] Structural Diversity of Metallothionein Revealed by Using Molecular Dynamics Simulations2021
- Author(s)
  Rikuri Morita, Yasuteru Shigeta, Ryuhei Harada
- Organizer
  第44回日本分子生物学会
- Data Source
  KAKENHI-PROJECT-21K06094
[Presentation] 分子動力学計算で解明するメタロチオネインの構造多様性2021
- Author(s)
  森田陸離, 重田育照, 原田隆平
- Organizer
  新学術領域研究「生命金属科学」領域会議第４回地方巡業（東京）
- Data Source
  KAKENHI-PROJECT-21K06094
[Presentation] 統計モデルを用いた天然変性領域の特徴抽出のための新たなスコア2021
- Author(s)
  會田勇斗, 原田隆平, 重田育照, 富井健太郎
- Organizer
  第21回日本蛋白質科学会年会
- Data Source
  KAKENHI-PROJECT-21K06094
[Presentation] Elucidation of Dnmt1 Activation Mechanism by Ubiquitinated Histones Using Molecular Dynamics Simulations2021
- Author(s)
  Takunori Yasuda, Rikuri Morita, Yasuteru Shigeta, Ryuhei Harada
- Organizer
  第44回日本分子生物学会
- Data Source
  KAKENHI-PROJECT-21K06094
[Presentation] 分子混雑のシミュレーション研究とカスケード選択型分子動力学シミュレーションの開発 (日本物理学会第13回若手奨励賞 -領域12- 受賞記念講演)2019
- Author(s)
  原田隆平
- Organizer
  日本物理学会2019年春季大会
- Invited
- Data Source
  KAKENHI-PROJECT-16H06164
[Presentation] Developments of Efficient Conformational Sampling Methods for Biogogically Rare Events2018
- Author(s)
  Ryuhei Harada
- Organizer
  Asia Hub for e-Drug Discovery (AHeDD) 2018
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-16H06164
[Presentation] カスケード型並列分子動力学シミュレーションとマルコフ状態モデルを併用したタンパク質の自由エネルギー計算2018
- Author(s)
  原田隆平, 重田育照
- Organizer
  日本物理学会2018年秋季大会
- Data Source
  KAKENHI-PROJECT-16H06164
[Presentation] 生物学的レアイベントを再現予測するタンパク質構造サンプリグ法の開発2018
- Author(s)
  原田隆平, 重田育照
- Organizer
  日本物理学会第73回年次大会
- Data Source
  KAKENHI-PROJECT-16H06164
[Presentation] 生物学的レアイベントを再現予測するタンパク質構造サンプリグ法の開発2018
- Author(s)
  原田隆平
- Organizer
  第２回ワークショップ「レアイベントの計算科学」
- Invited
- Data Source
  KAKENHI-PROJECT-16H06164
[Presentation] 生体分子シミュレーションによる機能解析と計算生体分子医科学への展開2018
- Author(s)
  原田隆平
- Organizer
  筑波大学計算科学研究センター計算メディカルサイエンス　キックオフシンポジウム
- Invited
- Data Source
  KAKENHI-PROJECT-16H06164
[Presentation] タンパク質の機能発現を解明する分子混雑シミュレーション手法およびカスケード型超並列シミュレーション手法の開発2018
- Author(s)
  原田隆平
- Organizer
  第98回日本化学会春季大会第67回日本化学会進歩賞受賞講演
- Invited
- Data Source
  KAKENHI-PROJECT-16H06164
[Presentation] データ駆動型分子動力学法による構造細密化と遷移構造探索2018
- Author(s)
  重田育照, 原田隆平
- Organizer
  第41回ケモインフォマティクス討論会
- Data Source
  KAKENHI-PROJECT-16H06164
[Presentation] 生物学的レアイベントを効率的に再現・予測する構造サンプリング手法の開発2017
- Author(s)
  原田隆平
- Organizer
  物性研究所スパコン共同利用 CCMS合同研究会「計算物質科学の今と未来」
- Invited
- Data Source
  KAKENHI-PROJECT-16H06164
[Presentation] 生物学的レアイベントを再現/予測する効率的構造サンプリング手法の開発2017
- Author(s)
  原田隆平
- Organizer
  新学術領域「柔らかな分子系」ワークショップ「若手研究者が描く分子理論の未来」
- Invited
- Data Source
  KAKENHI-PROJECT-16H06164
[Presentation] 生物学的レアイベントを再現 / 予測するタンパク質構造サンプリング手法の開発2017
- Author(s)
  原田隆平, 重田育照
- Organizer
  第17回日本蛋白質科学会年会
- Data Source
  KAKENHI-PROJECT-16H06164
[Presentation] 生物学的レアイベントを再現/予測する効率的構造サンプリング手法の開発2017
- Author(s)
  原田隆平
- Organizer
  第3回近電セミナー (物理工学懇談会協賛, 化学生命系セミナー協賛)
- Invited
- Data Source
  KAKENHI-PROJECT-16H06164
[Presentation] 生物学的レアイベントを再現する効率的構造サンプリング手法の開発2016
- Author(s)
  原田隆平, 重田育照
- Organizer
  第54回に本生物物理学会年会
- Invited
- Data Source
  KAKENHI-PROJECT-16H06164
[Presentation] レアイベント探索手法で探求するタンパク質フォールディングの普遍性2016
- Author(s)
  原田隆平, 鷹野優, 重田育照
- Organizer
  第16回日本蛋白質科学会年会
- Data Source
  KAKENHI-PROJECT-16H06164
[Presentation] カスケード型超並列シミュレーションを用いた生物学的レアイベント探索手法の構築2016
- Author(s)
  原田隆平
- Organizer
  凝縮系の理論化学2016
- Place of Presentation
  琉球大学(沖縄県中頭群西原町)
- Year and Date
  2016-03-10
- Invited
- Data Source
  KAKENHI-PROJECT-26840056
[Presentation] 生物学的レアイベントを再現する構造サンプリング手法の開発2016
- Author(s)
  原田隆平, 重田育照
- Organizer
  第30回分子シミュレーション討論会
- Data Source
  KAKENHI-PROJECT-16H06164
[Presentation] 逆状態分布に基づく効率的タンパク質構造サンプリング手法の開発2015
- Author(s)
  原田隆平, 鷹野優, 重田育照
- Organizer
  第29回分子シミュレーション討論会
- Place of Presentation
  朱鷺メッセ(新潟県新潟市)
- Year and Date
  2015-11-30
- Data Source
  KAKENHI-PROJECT-26840056
[Presentation] レアイベント探索手法"OFLOOD"で解明するタンパク質フォールディング機構2015
- Author(s)
  原田隆平, 鷹野優, 重田育照
- Organizer
  第15回日本蛋白質科学会年会
- Place of Presentation
  あわぎんホール(徳島県徳島市)
- Year and Date
  2015-06-24
- Data Source
  KAKENHI-PROJECT-26840056
[Presentation] Simple, yet Powerful Conformational Sampling Methodologies for Proteins2015
- Author(s)
  原田隆平, 鷹野優, 重田育照
- Organizer
  環太平洋化学会議 Pacifichem 2015
- Place of Presentation
  ハワイコンベンションセンター(米国ハワイ市)
- Year and Date
  2015-12-15
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-26840056
[Presentation] Simple yet Powerful Conformational Sampling Methods for Reproducing Biologically Rare Events2015
- Author(s)
  原田隆平
- Organizer
  第53回日本生物物理学会年会
- Place of Presentation
  金沢大学角間キャンパス(石川県金沢市)
- Year and Date
  2015-09-13
- Invited
- Data Source
  KAKENHI-PROJECT-26840056
[Presentation] タンパク質レアイベント抽出のための効率的構造サンプリング手法
- Author(s)
  原田隆平, 鷹野優, 重田照育
- Organizer
  第28回分子シミュレーション討論会
- Place of Presentation
  宮城県仙台市/仙台市民会館
- Year and Date
  2014-11-11 – 2014-11-14
- Data Source
  KAKENHI-PROJECT-26840056
[Presentation] 蛋白質構造揺らぎを用いた構造変化加速法 :FFM
- Author(s)
  原田隆平, 鷹野優, 重田照育
- Organizer
  第14回日本蛋白質科学会年会
- Place of Presentation
  神奈川県横浜市/ワークピア横浜
- Year and Date
  2014-06-25 – 2014-06-27
- Data Source
  KAKENHI-PROJECT-26840056
[Presentation] 大規模構造変化を誘起するMD手法を利用したナイロンオリゴマー分解酵素の誘導適合過程の解明
- Author(s)
  馬場剛史, 原田隆平, 中野雅由, 重田育照
- Organizer
  第17回理論化学討論会
- Place of Presentation
  愛知県名古屋市/名古屋大学東山キャンパス
- Year and Date
  2014-05-22 – 2014-05-24
- Data Source
  KAKENHI-PROJECT-26840056
[Presentation] タンパク質レアイベントを抽出する効率的構造サンプリング法
- Author(s)
  原田隆平, 鷹野優, 重田照育
- Organizer
  第52回日本生物物理学会年会
- Place of Presentation
  北海道札幌市/札幌コンベンションセンター
- Year and Date
  2014-09-25 – 2014-09-27
- Data Source
  KAKENHI-PROJECT-26840056
[Presentation] 酵素の基質結合と大規模構造変化に関する理論的研究
- Author(s)
  馬場剛史, 原田隆平, 中野雅由, 重田育照
- Organizer
  第8回分子科学討論会2014東広島
- Place of Presentation
  広島県東広島市/広島大学東広島キャンパス
- Year and Date
  2014-09-21 – 2014-09-23
- Data Source
  KAKENHI-PROJECT-26840056
[Presentation] ナイロンオリゴマー分解酵素の大規模構造変化に対するアミノ酸変異導入の効果
- Author(s)
  馬場剛史, 原田隆平, 中野雅由, 重田育照
- Organizer
  第14回日本蛋白質科学会年会
- Place of Presentation
  神奈川県横浜市/ワークピア横浜
- Year and Date
  2014-06-25 – 2014-06-27
- Data Source
  KAKENHI-PROJECT-26840056

1. 松村浩由 (30324809)

# of Collaborated Projects: 1 results

# of Collaborated Products: 1 results
2. 深山浩 (60373255)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
3. SHIGETA yasuteru

# of Collaborated Projects: 0 results

# of Collaborated Products: 15 results
4. ISHIKAWA Tomoko

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results
5. MURAKAWA Takeshi

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results
6. SHOJI mitsuo

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results
7. 鷹野優

# of Collaborated Projects: 0 results

# of Collaborated Products: 7 results
8. 杉田有治

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results
9. 立川仁典

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results
10. 北尾彰朗

# of Collaborated Projects: 0 results

# of Collaborated Products: 2 results
11. 林秀行

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results
12. 小川亜希子

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results
13. 吉野龍ノ介

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results

Harada Ryuhei 原田 隆平

Research Projects

Research Products

Co-Researchers

薬効発揮に重要な長時間ダイナミクスを抽出・解析する分子シミュレーション手法の開発Principal Investigator

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Identification of structural factors to improve Rubisco

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Prediction of Protein Dynamics Based on a Combination of Molecular Dynamics Simulation and Machine LearningPrincipal Investigator

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Signal Transduction Process of G-Protein Coupled Receptor (GPCR) Studied by Molecular Dynamics SimulationPrincipal Investigator

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Developments of methods for predicting transitions of proteins based on structural fluctuationsPrincipal Investigator

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[Journal Article] Design of electron-donating group substituted 2-PAM analogs as antidotes for organophosphate insecticide poisoning2023

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[Journal Article] Determination of the Association between Mesotrione Sensitivity and Conformational Change of 4-Hydroxyphenylpyruvate Dioxygenase via Free-Energy Analyses2023

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[Journal Article] Pathological mutations promote proteolysis of mitochondrial tRNA-specific 2-thiouridylase 1 (MTU1) via mitochondrial caseinolytic peptidase (CLPP)2023

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[Journal Article] Efficient Screening of Protein-Ligand Complexes in Lipid Bilayers Using LoCoMock Score2023

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[Journal Article] Free-energy Profiles for Membrane Permeation of Compounds Calculated Using Rare-Event Sampling Methods2023

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[Journal Article] A Structural Refinement Technique for Protein-RNA Complexes Based on a Combination of AI-based Modeling and Flexible Docking: A Study of Musashi-1 Protein2023

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[Journal Article] Latrunculin resistance mechanism of non‐conventional actin NAP1 uncovered by molecular dynamics simulations2023

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[Journal Article] A Variety of Initial Velocities in Restarting Molecular Dynamics Simulations Promotes Protein Transitions2023

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[Journal Article] Promising SARS-CoV-2 Main Protease Inhibitor Ligand-Binding Modes Evaluated Using LB-PaCS-MD/FMO2022

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[Journal Article] Protein Structure Validation Derives a Smart Conformational Search in a Physically Relevant Configurational Subspace2022

Harada Ryuhei 原田隆平