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J-GLOBAL ID：200901096092851040 Update date: Apr. 23, 2025

Kitao Akio

キタオアキオ | Kitao Akio

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Affiliation and department：
Job title： Professor
Homepage URL (2)： http://www.kitao.bio.titech.ac.jp/ , http://www.kitao.bio.titech.ac.jp/indexE.html

Research field (3)： Basic physical chemistry , Bio-, chemical, and soft-matter physics , Biophysics

Research keywords (24)： energy landscape , solvation , function , dynamics , molecular simulation , nano machine , Protein , 分子論 , 相互作用 , 分子メカニズム , 超並列計算 , 生体分子機械 , エネルギー地形 , 水和 , 機能 , ダイナミクス , 分子シミュレーション , ナノマシン , 蛋白質 , Theoretical Chemistry , Computational Chemistry , Computational Physics , Chemical Physics , Biophysics

Research theme for competitive and other funds (44)：

2024 - 2029 Generative design of protein molecular functions by molecular simulations
2023 - 2027 Investigating molecular interactions of p53 regulated by post translation modifications and intrinsically disordered regions with advanced simulation
2024 - 2026 Molecular mechanisms of non-domain biopolymers investigated by highly efficient molecular simulation
2023 - 2026 Structural analysis of the recognition mechanism of diverse chemicals by taste receptors
2023 - 2025 Quantitative prediction of the interactions involved in material symbiosis using advanced simulation

2022 - 2024 Analysis of free energy landscape, pathways, and flow of structural changes to complement high-speed molecular movie

2021 - 2023 Predicting effects of "weak interactions" quantitatively using advanced simulation

2020 - 2023 プレシジョンメディスンを加速する創薬ビッグデータ統合システムの推進

2019 - 2023 Investigating ligand-controlled GPCR activation mechanisms by cutting edge simulation

2020 - 2022 Complementation of molecular movie using analyses of free energy landscape of conformational change, pathway and flux

2017 - 2020 Reconsitutive studies on molecular mechanisms underlying regulation of rotational molecular machines

2014 - 2020 生体分子システムの機能制御による革新的創薬基盤の構築

2018 - 2019 Studying the Function of Soft Molecular Systems by the Concerted Use of Theory and Experiment

2015 - 2019 Flexibility, interactions, and function control mechanisms in multi-domain proteins

2015 - 2018 Support for International Activities of Studying the Function of Soft Molecular Systems by Concerted Use of Theory and Experiment

2013 - 2018 Studying the Function of Soft Molecular Systems by Concerted Use of Theory and Experiment

2013 - 2018 Softness-function relationship in large molecules and molecular assemblies investigated at atomic resolution

2007 - 2012 バイオ分子間相互作用形態の階層的モデリング

2011 - 2011 タンパク質複合体形成・解離に関わるモードカップリング解析法開発

2011 - 2011 Structure modeling and functional analysis of rotary motor state proteins based on mutational information

2009 - 2010 X線散漫散乱による生体分子の動的構造決定に向けた理論基盤の構築

2007 - 2010 Roles of hyper-anisotropic dynamics and frustration on protein function investigated in sub-msec order

2006 - 2010 既知ナノ生体物質の機能メカニズム解明」

2004 - 2009 Development of simulation methods for biological supramolecular structure and function analyses

2004 - 2009 Functional Mechanism and Structural Organization of Biological Macromolecular Assemblies

2007 - 2008 実験び理論的アプローチから得られる蛋白質ダイナミクス情報の相関マッピング

2007 - 2008 分子シミュレーションで探るABCトランスポーターの膜輸送動力発生機構

2006 - 2007 構造変化における蛋白質のエネルギー地形階層性と水和の役割

2003 - 2007 Roles of energy landscape hierarchy and hydration structure change in molecular recognition in protein

2003 - 2006 Underlying mechanism of bio-nano-machine investigated by massive molecular dynamics method

2002 - 2006 Functional analysis of bio-nano machine studied by molecular dynamics simulation

2004 - 2005 分子認識における蛋白質のエネルギー地形階層性と水和構造変化の役割

2001 - 2004 Prediction of structure and function of protein complexes

1999 - 2001 Mechanism of the CD2/CD58 complex formation in immune system

1999 - 2001 Energy Transfer in a Protein Molecule: From Chemical Reaction to Structural Change

2000 - 2000 構造ゲノム情報からの蛋白質のやわらかさと機能の関係を探る

1995 - 1999 Administration of researches on principles of protein architecture

1997 - 1998 タンパク質のエネルギー面階層性とモードカップリング

1995 - 1998 タンパク質立体構造の安定性・ダイナミックス・折れたたみ機構

1994 - 1995 Dynamics of the Electron Transfer Reaction in Cytochrome b_5

蛋白質分子の設計

タンパク質の複合体形成原理

タンパク質の立体構造安定性

タンパク質のダイナミックス

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Papers (128)：

Yiwei Liu, Takahiro Mori, Yusei Ito, Kimiko Kuroki, Seiichiro Hayashi, Daisuke Kohda, Taro Shimizu, Tatsuhiro Ishida, Steve R. Roffler, Mika K. Kaneko, et al. The strategy used by naïve anti-PEG antibodies to capture flexible and featureless PEG chains. Journal of Controlled Release. 2025. 380. 396-403
Shigeyuki Matsumoto, Yuta Isaka, Ryo Kanada, Biao Ma, Mitsugu Araki, Shuntaro Chiba, Atsushi Tokuhisa, Hiroaki Iwata, Shoichi Ishida, Yoshinobu Akinaga, et al. Precision spatiotemporal analysis of large-scale compound-protein interactions through molecular dynamics simulation. PNAS Nexus. 2025
Louis-Philippe Picard, Alexander Orazietti, Duy Phuoc Tran, Andrejs Tucs, Sari Hagimoto, Zhenzhou Qi, Shuya Kate Huang, Koji Tsuda, Akio Kitao, Adnan Sljoka, et al. Balancing G protein selectivity and efficacy in the adenosine A2A receptor. Nature Chemical Biology. 2024. 21. 1. 71-79
Shinji Ikizawa, Tatsuki Hori, Tegar Nurwahyu Wijaya, Hiroshi Kono, Zhen Bai, Tatsuhiro Kimizono, Wenbo Lu, Duy Phuoc Tran, Akio Kitao. PaCS-Toolkit: Optimized Software Utilities for Parallel Cascade Selection Molecular Dynamics (PaCS-MD) Simulations and Subsequent Analyses. The Journal of Physical Chemistry B. 2024. 128. 3631-3642
Tegar N. Wijaya, Akio Kitao. Energetic and Kinetic Origins of CALB Interfacial Activation Revealed by PaCS-MD/MSM. The Journal of Physical Chemistry B. 2023. 127. 7431-7441

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MISC (132)：

畑宏明, 北尾彰朗. Regulation of Bacterial Flagellar Motor Rotation using High Pressure. 高圧力の科学と技術. 2023. 33. 2
大沢陸輝, 寺原直矢, 古寺哲幸, 今田勝巳, 南野徹, 北尾彰朗. FlhAcの高速原子間力顕微鏡画像の解析. 分子シミュレーション討論会講演要旨集. 2022. 36th
Duy Phuoc TRAN, Akio KITAO. Calculation of Binding Free Energy and Kinetic Rates with Flexible Protein Docking. Seibutsu Butsuri. 2021. 61. 6. 398-399
Duy Phuoc Tran, Hiroaki Hata, Takumi Ogawa, Yuta Taira, Akio Kitao. PaCS-MD/MSM: Parallel Cascade Selection Molecular Dynamic Simulation in Combination with Markov State Model as an Efficient non-Bias Sampling Method. Ensemble. 2020. 22. 2. 151-156
Takemura Kazuhiro, Hata Hiroaki, Kitao Akio. Association and Dissociation Mechanisms of Protein Complexes and Complex Structure Prediction. Butsuri. 2019. 74. 8. 533-541

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Patents (1)：

FLAGELLAR AN DNEEDLE COMPLEX(INJECTOSOME)LOOP AS ANTI BACTERIAL DRUG TARGET,

Books (7)：

in silico創薬におけるスクリーニングの高速化・高精度化技術
技術情報協会 2018 ISBN:9784861046889
The Bacterial Flagellum
Springer 2017
揺らぎ・ダイナミクスと生体機能 : 物理化学的視点から見た生体分子
化学同人 2013 ISBN:9784759815108
シミュレーション辞典
コロナ社 2012 ISBN:9784339024586
Normal mode analysis : theory and applications to biological and chemical systems
Chapman & Hall/CRC 2006 ISBN:158488472X

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Lectures and oral presentations (143)：

SARS-CoV-2タンパク質のオリゴマー化を阻害する薬剤候補分子の探索
(新型コロナウイルス感染症対応HPCI臨時課題の最前線 2020)
PaCS-MDによるタンパク質-タンパク質複合体の解離シミュレーション
(第9回日本生物物理学会関東支部会 2020)
PaCS-MDによるアクトミオシンの結合解離予測
(第9回日本生物物理学会関東支部会 2020)
長時間ダイナミクス法と標的分子ネットワーク
(第7回重点課題1ワークショップ 2020)
計算で予測するタンパク質複合体立体構造と結合親和性
(第7回生命理工オープンイノベーションハブ(LiHub)フォーラム -メゾスケール分子と創薬- 2019)

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Works (21)：

PaCS-Toolkit
Shinji Ikizawa, Tatsuki Hori, Tegar Nurwahyu Wijaya, Hiroshi Kono, Zhen Bai, Tatsuhiro Kimizono, Wenbo Lu, Duy Phuoc Tran, Akio Kitao 2024 - 現在
eePaCS-MD (Edge expansion parallel cascade selection molecular dynamics)
Kenichiro Takaba, Duy Phuoc Tran, Akio Kitao 2020 -
a/dPaCS-MD (association and dissociation PaCS-MD)
Duy Phuoc Tran, Akio Kitao 2020 -
evERdock BAI (Machine-learning-guided selection of protein-protein complex structure)
Kei Terayama, Ai Shinbu, Koji Tsuda, Kazuhiro Takemura, Akio Kitao 2019 -
dPaCS-MD/MSM
Duy Phuoc Tran, Akio Kitao 2019 -

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Education (3)：

1991 - 1993 Kyoto University Graduate School of Science Department of Chemictry Doctor Course
1989 - 1991 Kyoto University Graduate School of Science Department of Chemictry Master Course
1985 - 1989 Kyoto University Faculty of Science Mainly Physics and Chemistry

Professional career (3)：

Doctor of Science (Kyoto University)
Master of Science (Kyoto University)
Bachelor of Science (Kyoto University)

Work history (12)：

2024/10 - 現在 Institute of Science Tokyo School of Life Science and Technology Professor
2016/04 - 現在 National Institutes for Quantum and Radiological Science and Technology Adjunct Researcher
2017/07 - 2024/09 Tokyo Institute of Technology School of Life Science and Technology Professor
2017/07 - 2018/03 The University of Tokyo Institute of Molecular and Cellular Biosciences "Ishoku" Professor
2007/04 - 2017/06 The University of Tokyo Institute of Molecular and Cellular Biosciences Associate Professor

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Committee career (22)：

2025/01 - 現在分子シミュレーション学会事務局長
2023/04 - 現在日本物理学会代議員
2008 - 現在日本蛋白質科学会男女共同参画ワーキンググループ
2021/01 - 2024/12 日本シミュレーション学会編集委員長
2023/04 - 2024/03 日本物理学会領域委員会委員

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Association Membership(s) (10)：

Chemical Information and Computer Science The Chemical Society of Japan , 日本化学会情報化学部会 , Biophysical Society , Protein Science Society of Japan , The physical Society of Japan , 溶液化学研究会 , The Chemical Society of Japan , The biophysical Society of Japan , 日本分子シミュレーション学会 , American Chemical Society

※ Researcher’s information displayed in J-GLOBAL is based on the information registered in researchmap. For details, see here.

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