Okazaki Kei-ichi 岡崎圭一

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Kei-ichi Okazaki 岡崎圭一

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Researcher Number	50792529
Other IDs
Affiliation (Current)	2026: 大学共同利用機関法人自然科学研究機構(岡崎共通研究施設), 計算科学研究センター, 准教授
Affiliation (based on the past Project Information) *help	2022 – 2025: 大学共同利用機関法人自然科学研究機構(岡崎共通研究施設), 計算科学研究センター, 准教授 2020: 大学共同利用機関法人自然科学研究機構(岡崎共通研究施設), 計算科学研究センター, 准教授 2018 – 2019: 分子科学研究所, 理論・計算分子科学研究領域, 特任准教授
Review Section/Research Field	Principal Investigator Basic Section 43040:Biophysics-related / Transformative Research Areas, Section (II)
Keywords	Principal Investigator 分子シミュレーション / 生体分子モーター / ATP合成酵素 / 構造予測AI / AlphaFold / GTP / 生体分子マシン / ダイナミン / 細胞膜変形分子マシン / GTP加水分解 … More / 構造変化 / 細胞膜 / 粗視化モデル / 生体膜マイクロチップ / 疎水性ゲート / 基質輸送速度 / 遷移パス / 分子動力学シミュレーション / トランスポーター Less

Integration of AlphaFold and molecular simulation for controlling conformational change of biomolecular motorsPrincipal Investigator
- Principal Investigator
  
  岡崎圭一
- Project Period (FY)
  2025 – 2026
- Research Category
  
  Grant-in-Aid for Transformative Research Areas (A)
- Review Section
  
  Transformative Research Areas, Section (II)
- Research Institution
  Okazaki Research Facilities, National Institutes of Natural Sciences
Mechanism of membrane-transforming biomolecular machines: Theoretical study of their oligomerization and conformational changePrincipal Investigator
- Principal Investigator
  
  岡崎圭一
- Project Period (FY)
  2024 – 2025
- Research Category
  
  Grant-in-Aid for Scientific Research (B)
- Review Section
  
  Basic Section 43040:Biophysics-related
- Research Institution
  Okazaki Research Facilities, National Institutes of Natural Sciences
Theoretical prediction of mutations that speed up substrate transportation in transporter proteinPrincipal Investigator
- Principal Investigator
  
  Kei-ichi Okazaki
- Project Period (FY)
  2018 – 2020
- Research Category
  
  Grant-in-Aid for Scientific Research (B)
- Review Section
  
  Basic Section 43040:Biophysics-related
- Research Institution
  Okazaki Research Facilities, National Institutes of Natural Sciences
  Institute for Molecular Science

All 2025 2024 2023 2022 2021 2020 2019 2018

All Journal Article Presentation

[Journal Article] Investigating the hyperparameter space of deep neural network models for reaction coordinates2025
- Author(s)
  Kawashima Kyohei、Sato Takumi、Okazaki Kei-ichi、Kim Kang、Matubayasi Nobuyuki、Mori Toshifumi
- Journal Title
  
  APL Machine Learning
  
  Volume: 3 Issue: 1 Pages: 1-11
- DOI
  10.1063/5.0252631
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-23K23303, KAKENHI-PROJECT-23K23858, KAKENHI-PROJECT-23K27313, KAKENHI-PROJECT-22K03550, KAKENHI-PROJECT-24K21756, KAKENHI-PROJECT-23KK0254
[Journal Article] Unveiling interatomic distances influencing the reaction coordinates in alanine dipeptide isomerization: An explainable deep learning approach2024
- Author(s)
  Okada Kazushi、Kikutsuji Takuma、Okazaki Kei-ichi、Mori Toshifumi、Kim Kang、Matubayasi Nobuyuki
- Journal Title
  
  The Journal of Chemical Physics
  
  Volume: 160 Issue: 17 Pages: 1-8
- DOI
  10.1063/5.0203346
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-23K23303, KAKENHI-PROJECT-23K23858, KAKENHI-PROJECT-23K27313, KAKENHI-PROJECT-22K03550, KAKENHI-PROJECT-24K21756, KAKENHI-PROJECT-23KK0254
[Journal Article] Integration of AlphaFold with Molecular Dynamics for Efficient Conformational Sampling of Transporter Protein NarK2024
- Author(s)
  Ohnuki Jun、Okazaki Kei-ichi
- Journal Title
  
  The Journal of Physical Chemistry B
  
  Volume: 128 Issue: 31 Pages: 7530-7537
- DOI
  10.1021/acs.jpcb.4c02726
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-23K23858, KAKENHI-PROJECT-23K14160
[Journal Article] Accelerated Molecular Dynamics and AlphaFold Uncover a Missing Conformational State of Transporter Protein OxlT2024
- Author(s)
  Ohnuki Jun、Jaunet-Lahary Titouan、Yamashita Atsuko、Okazaki Kei-ichi
- Journal Title
  
  The Journal of Physical Chemistry Letters
  
  Volume: 15 Issue: 3 Pages: 725-732
- DOI
  10.1021/acs.jpclett.3c03052
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-23K14160, KAKENHI-PROJECT-23K23858
[Journal Article] Rotary mechanism of the prokaryotic Vo motor driven by proton motive force2024
- Author(s)
  Kishikawa Jun-ichi、Nishida Yui、Nakano Atsuki、Kato Takayuki、Mitsuoka Kaoru、Okazaki Kei-ichi、Yokoyama Ken
- Journal Title
  
  Nature Communications
  
  Volume: 15 Issue: 1 Pages: 9883-9883
- DOI
  10.1038/s41467-024-53504-x
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-23K23858, KAKENHI-PROJECT-23K27146
[Journal Article] Optimizing Go-MARTINI Coarse-Grained Model for F-BAR Protein on Lipid Membrane2021
- Author(s)
  Mahmood Md. Iqbal、Poma Adolfo B.、Okazaki Kei-ichi
- Journal Title
  
  Frontiers in Molecular Biosciences
  
  Volume: 8 Pages: 619381-619381
- DOI
  10.3389/fmolb.2021.619381
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-18H02415
[Journal Article] Learning reaction coordinates via cross-entropy minimization: Application to alanine dipeptide2020
- Author(s)
  Mori Yusuke、Okazaki Kei-ichi、Mori Toshifumi、Kim Kang、Matubayasi Nobuyuki
- Journal Title
  
  The Journal of Chemical Physics
  
  Volume: 153 Issue: 5 Pages: 054115-054115
- DOI
  10.1063/5.0009066
- Peer Reviewed
- Data Source
  KAKENHI-PUBLICLY-20H05221, KAKENHI-PROJECT-18H02415, KAKENHI-PROJECT-19H04206, KAKENHI-PROJECT-18K05049, KAKENHI-PROJECT-18H01188
[Journal Article] Chemical-State-Dependent Free Energy Profile from Single-Molecule Trajectories of Biomolecular Motors: Application to Processive Chitinase2020
- Author(s)
  Okazaki Kei-ichi、Nakamura Akihiko、Iino Ryota
- Journal Title
  
  The Journal of Physical Chemistry B
  
  Volume: 124 Issue: 30 Pages: 6475-6487
- DOI
  10.1021/acs.jpcb.0c02698
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-18H02415, KAKENHI-PROJECT-18H02418
[Journal Article] Chitinase Moves on and Degradates Crystalline Chitin with Brownian Motion2019
- Author(s)
  NAKAMURA Akihiko、OKAZAKI Kei-ichi、FURUTA Tadaomi、SAKURAI Minoru、IINO Ryota
- Journal Title
  
  Seibutsu Butsuri
  
  Volume: 59 Issue: 6 Pages: 330-333
- DOI
  10.2142/biophys.59.330
- NAID
  130007750992
- ISSN
  0582-4052, 1347-4219
- Language
  Japanese
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-18H02415
[Journal Article] Curvature induction and sensing of the F-BAR protein Pacsin1 on lipid membranes via molecular dynamics simulations2019
- Author(s)
  Mahmood Md. Iqbal、Noguchi Hiroshi、Okazaki Kei-ichi
- Journal Title
  
  Scientific Reports
  
  Volume: 9 Issue: 1 Pages: 14557-14557
- DOI
  10.1038/s41598-019-51202-z
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-18H02415
[Journal Article] Mechanism of the electroneutral sodium/proton antiporter PaNhaP from transition-path shooting2019
- Author(s)
  Okazaki Kei-ichi、Wohlert David、Warnau Judith、Jung Hendrik、Yildiz Ozkan、Kuhlbrandt Werner、Hummer Gerhard
- Journal Title
  
  Nature Communications
  
  Volume: 10 Issue: 1 Pages: 1742-1742
- DOI
  10.1038/s41467-019-09739-0
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-18H02415
[Journal Article] Ion Binding and Selectivity of the Na+/H+ Antiporter MjNhaP1 from Experiment and Simulation2019
- Author(s)
  Warnau Judith、Wohlert David、Okazaki Kei-ichi、Yildiz Ozkan、Gamiz-Hernandez Ana P.、Kaila Ville R. I.、Kuhlbrandt Werner、Hummer Gerhard
- Journal Title
  
  The Journal of Physical Chemistry B
  
  Volume: 124 Issue: 2 Pages: 336-344
- DOI
  10.1021/acs.jpcb.9b08552
- Peer Reviewed / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-18H02415
[Presentation] 分子シミュレーションとAlphaFoldの統合によるトランスポータータンパク質の構造変化ダイナミクス解明2025
- Author(s)
  岡崎圭一
- Organizer
  第463回CBI学会講演会「分子シミュレーションの最新動向　～構造・ダイナミクス解析から機能解析まで～」
- Invited
- Data Source
  KAKENHI-PROJECT-23K23858
[Presentation] AlphaFoldと分子シミュレーションの統合によるタンパク質機能発現ダイナミクスの解明2025
- Author(s)
  岡崎圭一
- Organizer
  日本化学会第105春期年会・次世代分子システム化学のフロンティア―協奏的機能発現の素過程的理解
- Invited
- Data Source
  KAKENHI-PROJECT-23K23858
[Presentation] Molecular Simulation and Statistical Inference of Functional Motions of Biomolecular Machines2023
- Author(s)
  Kei-ichi Okazaki
- Organizer
  The 5th R-CCS International Symposium: Fugaku and Beyond
- Invited
- Data Source
  KAKENHI-PROJECT-23K23858
[Presentation] Dynamin-1 assembly and membrane tubule constriction mechanism revealed by coarse-grained simulations2023
- Author(s)
  Md. Iqbal Mahmood, Shintaroh Kubo, and Kei-ichi Okazaki
- Organizer
  第61回日本生物物理学会年会
- Data Source
  KAKENHI-PROJECT-23K23858
[Presentation] Conformational dynamics of transporter proteins revealed by molecular simulation and AlphaFold22023
- Author(s)
  Kei-ichi Okazaki
- Organizer
  第61回日本生物物理学会年会
- Invited
- Data Source
  KAKENHI-PROJECT-23K23858
[Presentation] Coarse-grained simulations of curvature induction and sensing of the F-BAR protein Pacsin1 on lipid membranes2022
- Author(s)
  Kei-ichi Okazaki
- Organizer
  The 6th Telluride Workshop on Coarse-Grained Modeling of Structure and Dynamics of Biomacromolecules
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-23K23858
[Presentation] 生体分子マシンにおける機能発現ダイナミクスの解明とその制御2021
- Author(s)
  岡崎圭一
- Organizer
  第1回生体分子シミュレーション・モデリング研究会
- Data Source
  KAKENHI-PROJECT-18H02415
[Presentation] Mechanism of Na+/H+ antiporter from transition path sampling and engineering of a faster transporter2020
- Author(s)
  Kei-ichi Okazaki
- Organizer
  Frontiers of Computational Physics from meV to MeV
- Invited
- Data Source
  KAKENHI-PROJECT-18H02415
[Presentation] 分子モーターの１方向性運動モデルの新規推定法の開発 ―キチナーゼへの応用2020
- Author(s)
  岡崎圭一
- Organizer
  第10回分子モーター討論会
- Data Source
  KAKENHI-PROJECT-18H02415
[Presentation] Curvature induction and sensing of the F-BAR protein Pacsin1 on lipid membranes via molecular dynamics simulations2020
- Author(s)
  Kei-ichi Okazaki
- Organizer
  第58回日本生物物理学会年会
- Invited
- Data Source
  KAKENHI-PROJECT-18H02415
[Presentation] 遷移パスサンプリングによる膜輸送タンパク質の基質輸送メカニズムの解明2019
- Author(s)
  岡崎圭一
- Organizer
  スーパーコンピュータワークショップ2018
- Invited
- Data Source
  KAKENHI-PROJECT-18H02415
[Presentation] Molecular simulation and modeling of functional dynamics in FoF1 ATP synthase2019
- Author(s)
  Kei-ichi Okazaki
- Organizer
  2nd Tokyo ATPase Workshop
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-18H02415
[Presentation] Dynamic energy landscape of a linear motor chitinase from single-particle tracking trajectories2019
- Author(s)
  Kei-ichi Okazaki
- Organizer
  第57回日本生物物理学会年会
- Invited
- Data Source
  KAKENHI-PROJECT-18H02415
[Presentation] 生体分子マシンにおける機能ダイナミクスの解明2018
- Author(s)
  岡崎圭一
- Organizer
  生物物理若手の会第58回夏の学校
- Invited
- Data Source
  KAKENHI-PROJECT-18H02415
[Presentation] Transport mechanism of sodium/proton antiporter from transition-path simulations2018
- Author(s)
  Kei-ichi Okazaki
- Organizer
  the 2nd workshop on Advances in Theory and Computation of Complex Systems --- Biological Systems
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-18H02415
[Presentation] Mechanism of electroneutral sodium/proton antiporter from transition-path shooting2018
- Author(s)
  Kei-ichi Okazaki
- Organizer
  Institute Seminar, Max-Planck Institute of Biophysics
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-18H02415
[Presentation] Mechanism of Na+/H+ antiporter from transition-path simulations: Making faster transporter based on mechanism2018
- Author(s)
  Kei-ichi Okazaki
- Organizer
  Workshop: Trends in Computational Molecular Biophysics
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-18H02415

1. 渡邉力也 (30540108)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
2. KIM Kang

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results
3. 森俊文

# of Collaborated Projects: 0 results

# of Collaborated Products: 2 results
4. 大貫隼

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results

Okazaki Kei-ichi 岡崎 圭一

Kei-ichi Okazaki 岡崎 圭一

Research Projects

Research Products

Co-Researchers

Integration of AlphaFold and molecular simulation for controlling conformational change of biomolecular motorsPrincipal Investigator

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

Mechanism of membrane-transforming biomolecular machines: Theoretical study of their oligomerization and conformational changePrincipal Investigator

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

Theoretical prediction of mutations that speed up substrate transportation in transporter proteinPrincipal Investigator

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

[Journal Article] Investigating the hyperparameter space of deep neural network models for reaction coordinates2025

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Unveiling interatomic distances influencing the reaction coordinates in alanine dipeptide isomerization: An explainable deep learning approach2024

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Integration of AlphaFold with Molecular Dynamics for Efficient Conformational Sampling of Transporter Protein NarK2024

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Accelerated Molecular Dynamics and AlphaFold Uncover a Missing Conformational State of Transporter Protein OxlT2024

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Rotary mechanism of the prokaryotic Vo motor driven by proton motive force2024

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Optimizing Go-MARTINI Coarse-Grained Model for F-BAR Protein on Lipid Membrane2021

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Learning reaction coordinates via cross-entropy minimization: Application to alanine dipeptide2020

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Chemical-State-Dependent Free Energy Profile from Single-Molecule Trajectories of Biomolecular Motors: Application to Processive Chitinase2020

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Chitinase Moves on and Degradates Crystalline Chitin with Brownian Motion2019

Author(s)

Journal Title

DOI

NAID

ISSN

Language

Data Source

[Journal Article] Curvature induction and sensing of the F-BAR protein Pacsin1 on lipid membranes via molecular dynamics simulations2019

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Mechanism of the electroneutral sodium/proton antiporter PaNhaP from transition-path shooting2019

Author(s)

Journal Title

DOI

Okazaki Kei-ichi 岡崎圭一

Kei-ichi Okazaki 岡崎圭一