Koda Shin-ichi 甲田信一

Researcher Number	10790404
Other IDs	https://orcid.org/0000-0003-0993-3678
Affiliation (Current)	2026: 分子科学研究所, 理論・計算分子科学研究領域, 助教
Affiliation (based on the past Project Information) *help	2026: 分子科学研究所, 理論・計算分子科学研究領域, 助教 2018 – 2024: 分子科学研究所, 理論・計算分子科学研究領域, 助教
Review Section/Research Field	Principal Investigator Basic Section 32010:Fundamental physical chemistry-related
Keywords	Principal Investigator 反応モデル / 概日リズム / シアノバクテリア / 体内時計 / 最小エネルギー経路 / KaiB / 遷移状態探索 / 反応経路探索 / シミュレーション / 階層性 / ATP加水分解 / 数理モデル / 時計タンパク質

頑健かつ効率的な両端指定型経路探索に基づく錯体触媒反応機構の自動探索の基盤構築Principal Investigator
- Principal Investigator
  
  甲田信一
- Project Period (FY)
  2026 – 2029
- Research Category
  
  Grant-in-Aid for Scientific Research (C)
- Review Section
  
  Basic Section 32010:Fundamental physical chemistry-related
- Research Institution
  Institute for Molecular Science
シアノバクテリア時計タンパク質振動子の出力分子機構の理論的解明Principal Investigator
- Principal Investigator
  
  甲田信一
- Project Period (FY)
  2022 – 2025
- Research Category
  
  Grant-in-Aid for Early-Career Scientists
- Review Section
  
  Basic Section 32010:Fundamental physical chemistry-related
- Research Institution
  Institute for Molecular Science
Theoretical study of clock proteins focusing on cooperation of spatio-temporal dynamicsPrincipal Investigator
- Principal Investigator
  
  Koda Shin-ichi
- Project Period (FY)
  2018 – 2021
- Research Category
  
  Grant-in-Aid for Early-Career Scientists
- Review Section
  
  Basic Section 32010:Fundamental physical chemistry-related
- Research Institution
  Institute for Molecular Science

All 2025 2024 2022 2020 2018

All Journal Article Presentation

[Journal Article] Correlated Flat-Bottom Elastic Network Model for Improved Bond Rearrangement in Reaction Paths2025
- Author(s)
  Koda Shin-ichi、Saito Shinji
- Journal Title
  
  Journal of Chemical Theory and Computation
  
  Volume: 21 Issue: 7 Pages: 3513-3522
- DOI
  10.1021/acs.jctc.4c01549
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-23K17361, KAKENHI-PROJECT-22K14652
[Journal Article] Locating Transition States by Variational Reaction Path Optimization with an Energy-Derivative-Free Objective Function2024
- Author(s)
  Koda Shin-ichi、Saito Shinji
- Journal Title
  
  Journal of Chemical Theory and Computation
  
  Volume: 20 Issue: 7 Pages: 2798-2811
- DOI
  10.1021/acs.jctc.3c01246
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-22K14652, KAKENHI-PROJECT-21H04676, KAKENHI-PROJECT-23K17361
[Journal Article] Flat-Bottom Elastic Network Model for Generating Improved Plausible Reaction Paths2024
- Author(s)
  Koda Shin-ichi、Saito Shinji
- Journal Title
  
  Journal of Chemical Theory and Computation
  
  Volume: 20 Pages: 7176-7187
- DOI
  10.1021/acs.jctc.4c00792
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-23K17361, KAKENHI-PROJECT-22K14652
[Journal Article] Multimeric structure enables the acceleration of KaiB-KaiC complex formation induced by ADP/ATP exchange inhibition2022
- Author(s)
  Shin-ichi Koda, Shinji Saito
- Journal Title
  
  PLOS Computational Biology
  
  Volume: 18 Issue: 3 Pages: e1009243-e1009243
- DOI
  10.1371/journal.pcbi.1009243
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-18K14185, KAKENHI-PROJECT-21H04676
[Journal Article] An alternative interpretation of the slow KaiB-KaiC binding of the cyanobacterial clock proteins2020
- Author(s)
  Koda Shin-ichi、Saito Shinji
- Journal Title
  
  Scientific Reports
  
  Volume: 10 Issue: 1 Pages: 10439-10439
- DOI
  10.1038/s41598-020-67298-7
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-18K14185, KAKENHI-PROJECT-16H02254
[Presentation] 尤もらしい反応経路を与える構造ベースの軽量なポテンシャルエネルギー2024
- Author(s)
  甲田信一、斉藤真司
- Organizer
  第18回分子科学討論会
- Data Source
  KAKENHI-PROJECT-22K14652
[Presentation] 高成功率かつ低計算量の両端固定型遷移状態探索2024
- Author(s)
  甲田信一、斉藤真司
- Organizer
  第26回理論化学討論会
- Data Source
  KAKENHI-PROJECT-22K14652
[Presentation] 非線形計画問題汎用ソルバを用いた最小エネルギー経路探索2022
- Author(s)
  甲田信一，斉藤真司
- Organizer
  第24回理論化学討論会
- Data Source
  KAKENHI-PROJECT-22K14652
[Presentation] 時計タンパク質KaiCの一方向的アロステリに関する反応モデル構築に基づく考察2018
- Author(s)
  甲田信一、斉藤真司
- Organizer
  第２１回理論化学討論会
- Data Source
  KAKENHI-PROJECT-18K14185

1. 齊藤真司

# of Collaborated Projects: 0 results

# of Collaborated Products: 2 results

Koda Shin-ichi 甲田 信一

Research Projects

Research Products

Co-Researchers

頑健かつ効率的な両端指定型経路探索に基づく錯体触媒反応機構の自動探索の基盤構築Principal Investigator

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

シアノバクテリア時計タンパク質振動子の出力分子機構の理論的解明Principal Investigator

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

Theoretical study of clock proteins focusing on cooperation of spatio-temporal dynamicsPrincipal Investigator

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

[Journal Article] Correlated Flat-Bottom Elastic Network Model for Improved Bond Rearrangement in Reaction Paths2025

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Locating Transition States by Variational Reaction Path Optimization with an Energy-Derivative-Free Objective Function2024

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Flat-Bottom Elastic Network Model for Generating Improved Plausible Reaction Paths2024

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Multimeric structure enables the acceleration of KaiB-KaiC complex formation induced by ADP/ATP exchange inhibition2022

Author(s)

Journal Title

DOI

Data Source

[Journal Article] An alternative interpretation of the slow KaiB-KaiC binding of the cyanobacterial clock proteins2020

Author(s)

Journal Title

DOI

Data Source

[Presentation] 尤もらしい反応経路を与える構造ベースの軽量なポテンシャルエネルギー2024

Author(s)

Organizer

Data Source

[Presentation] 高成功率かつ低計算量の両端固定型遷移状態探索2024

Author(s)

Organizer

Data Source

[Presentation] 非線形計画問題汎用ソルバを用いた最小エネルギー経路探索2022

Author(s)

Organizer

Data Source

[Presentation] 時計タンパク質KaiCの一方向的アロステリに関する反応モデル構築に基づく考察2018

Author(s)

Organizer

Data Source

Koda Shin-ichi 甲田信一