Updated on 2026/07/09

写真a

 
KITAO AKIO
 
Organization
School of Life Science and Technology Professor
Title
Professor
Profile
I have been invesigating functional mechanisms of biological nano-machines. For this purpose, simulations of the behavior of biological system including nano-machines and solvent molecules in silico in atomic detail by using molecular dynamics simulation are conducted.
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News & Topics

Degree

  • Doctor of Science ( 1994.3   Kyoto University )

  • Master of Science ( 1991.3   Kyoto University )

  • Bachelor of Science ( 1989.3   Kyoto University )

Research Interests

  • Protein dynamics, Computational biology, Biophysics, Computational chemistry

  • 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

  • energy landscape

  • solvation

  • function

  • dynamics

  • 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 Areas

  • Nanotechnology/Materials / Fundamental physical chemistry

  • Natural Science / Biophysics, chemical physics and soft matter physics

  • Life Science / Biophysics

Research History

  • Kyoto University   Graduate School of Science, Graduate School of Chemistry   Part-time Lecturer

    2025

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    Country:Japan

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  • Institute of Science Tokyo   School of Life Science and Technology   Professor

    2024.10

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    Country:Japan

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  • National Institutes for Quantum and Radiological Science and Technology   Adjunct Researcher

    2016.4

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Professional Memberships

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Committee Memberships

  • 分子シミュレーション学会   事務局長  

    2025.1   

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    Committee type:Academic society

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  • 日本物理学会   代議員  

    2023.4 - 2027.3   

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    Committee type:Academic society

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  • 日本蛋白質科学会   男女共同参画ワーキンググループ  

    2008 - 2025.9   

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    Committee type:Academic society

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Papers

  • In Vitro Evolution of the Adenosine A2A Receptor Based on an Antagonist Binding Using a Ribosome Display. Reviewed International journal

    Genki Fukasawa, Yuma Matsuoka, Duy Phuoc Tran, Haruka Nishigaki, Keisuke Fukunaga, Takayoshi Watanabe, Tomohiro Doura, Naohiro Terasaka, Ako Kagawa, Takeshi Murata, Akio Kitao, Shigeki Kiyonaka, Tomoaki Matsuura

    Journal of the American Chemical Society   2026.3

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    Authorship:Corresponding author   Language:English   Publishing type:Research paper (scientific journal)  

    In vitro evolution is one of the powerful methods for altering the characteristics of a protein of interest; however, its application to membrane proteins remains challenging due to the requirement of a membrane environment in vitro. This study presents the first successful in vitro evolution of human adenosine A2A receptor (A2AR), one of the G protein-coupled receptors (GPCRs), achieved through combining cell-free protein synthesis (CFPS), a nanodisc for membrane mimicry, and a ribosome display. A saturation mutagenesis library of A2AR targeting the L167 and L267 residues, a library with a diversity of only 400, was constructed without sequence bias. Three rounds of affinity selection against A2AR-selective antagonist ZM241385 enriched the L167N/L267A and L167N/L267S mutants. These mutants exhibited greater than 10-fold improved sensitivity to ZM241385 in mammalian cell-based assays while retaining responsiveness to the endogenous ligand adenosine. Molecular dynamics simulations revealed new interactions between ZM241385 and A2AR mutants that are likely to contribute to stabilizing the conformation of the complexes. Finally, as an example of an application, the obtained mutant was used for cell-type-specific inhibition of A2AR signaling by ZM241385. This study demonstrates a powerful strategy for engineering GPCRs entirely in vitro with tailored ligand-binding properties, even from a library with small diversity, and shows that the evolved mutants exhibit improved functionality in mammalian cells.

    File: in-vitro-evolution-of-the-adenosine-a2a-receptor-based-on-an-antagonist-binding-using-a-ribosome-display.pdf

    DOI: 10.1021/jacs.6c02372

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  • The role of the tryptophan-rich allosteric network and sodium egress in GPCR activation Reviewed

    Zhenzhou Qi, Duy Phuoc Tran, Andrejs Tučs, Roopan Thiara, Louis-Philippe Picard, Koji Tsuda, Aditya Pandey, Adnan Sljoka, Akio Kitao, Robert Scott Prosser

    Proceedings of the National Academy of Sciences   123 ( 10 )   2026.3

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    Authorship:Corresponding author   Language:English   Publishing type:Research paper (scientific journal)   Publisher:Proceedings of the National Academy of Sciences  

    The human adenosine A 2A receptor (A 2A R) is a prototypical member of the class A family of G Protein–Coupled Receptors (GPCRs), which are engaged by over one-third of FDA-approved drugs. Here, we used 19 F NMR to simultaneously evaluate functional states from the perspective of a CF 3 -tag on transmembrane helix-6 (TM6) and all 5-fluorotryptophan reporters. Whereas spectra from the TM6 tag reveal a dynamic conformational ensemble, the tryptophan spectra exhibit more discrete ligand-dependent states. These ligand-dependent signatures provide insights into microswitches including a universal toggle switch which interfaces with a sodium binding pocket. Over 560 GPCRs share this toggle switch — sodium pocket cluster, implying a fundamental role in activation. Computational rigidity-theory reveals tryptophan reporters reside along prominent allosteric activation pathways, underscoring their roles in mechanical signal propagation and corroborating NMR observations. Among them, W246 6.48 , associated with the toggle switch, plays a critical role in regulation of allosteric networks spanning the orthosteric pocket and extending via tryptophan-rich pathways through the receptor to the A 2A R-Gβ interface and the nucleotide pocket in G s α. While higher sodium concentrations (~100 mM) predictably stabilize the inactive conformation of the receptor, lower concentrations (below 40 mM) greatly enhanced the presence of the activation ensemble and in particular, the precoupled state, suggesting that the release of sodium from the conserved pocket—either through basal conditions for the apo receptor, or upon binding of the agonist—enables sampling of a precoupled state, ultimately needed to initiate activation and coupling.

    DOI: 10.1073/pnas.2525502123

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  • Tandem Allosteric Effects of Reactant and Product that Promote Deacetylation Cycles in Sir2 Reviewed International journal

    Zhen Bai, Duy Phuoc Tran, Akio Kitao

    Journal of Chemical Information and Modeling   65   11326 - 11341   2025.10

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    Authorship:Last author, Corresponding author   Language:English   Publishing type:Research paper (scientific journal)  

    File: tandem-allosteric-effects-of-reactant-and-product-that-promote-deacetylation-cycles-in-sir2.pdf

    DOI: 10.1021/acs.jcim.5c01755

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  • RNA Binding Mechanism of the FUS Zinc Finger in Concert with Its Flanking Intrinsically Disordered Region Reviewed

    Soichiro Kijima, Akio Kitao

    Journal of Chemical Information and Modeling   2025.8

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    Authorship:Last author, Corresponding author   Language:English   Publishing type:Research paper (scientific journal)  

    File: kijima-kitao-2025-rna-binding-mechanism-of-the-fus-zinc-finger-in-concert-with-its-flanking-intrinsically-disordered.pdf

    DOI: 10.1021/acs.jcim.5c01059

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  • Interactive Docking Workshop: Docking the Anticancer Drug Belinostat to Its Cellular Histone Deacetylase (HDAC) Target Reviewed

    Georgios Iakovou, L. Palmer, A. Ganesan, Akio Kitao, Stephen D. Laycock, Steven Hayward

    Journal of Chemical Education   2025.6

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    DOI: 10.1021/acs.jchemed.4c01347

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  • The strategy used by naïve anti-PEG antibodies to capture flexible and featureless PEG chains Reviewed International journal

    Yiwei Liu, Takahiro Mori, Yusei Ito, Kimiko Kuroki, Seiichiro Hayashi, Daisuke Kohda, Taro Shimizu, Tatsuhiro Ishida, Steve R. Roffler, Mika K. Kaneko, Yukinari Kato, Takao Arimori, Takamasa Teramoto, Kazuhiro Takemura, Kenta Ishibashi, Yoshiki Katayama, Katsumi Maenaka, Yoshimitsu Kakuta, Akio Kitao, Takeshi Mori

    Journal of Controlled Release   380   396 - 403   2025.4

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    Authorship:Corresponding author   Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1016/j.jconrel.2025.02.001

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  • Precision spatiotemporal analysis of large-scale compound–protein interactions through molecular dynamics simulation Reviewed

    Shigeyuki Matsumoto, Yuta Isaka, Ryo Kanada, Biao Ma, Mitsugu Araki, Shuntaro Chiba, Atsushi Tokuhisa, Hiroaki Iwata, Shoichi Ishida, Yoshinobu Akinaga, Kei Terayama, Ryosuke Kojima, Yohei Harada, Kazuhiro Takemura, Teruki Honma, Akio Kitao, Yasushi Okuno

    PNAS Nexus   2025.3

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:Oxford University Press (OUP)  

    Abstract

    Biological systems are composed of and regulated by intricate and diverse biomolecular interactions. Experimental and computational approaches have been developed to elucidate the mechanisms of these interactions; however, owing to cost, time, and accuracy issues, large-scale spatiotemporal analyses of molecular pairs remains challenging. Thus, the molecular recognition mechanisms underlying these diverse interactions remain unclear. We successfully simulated the large-scale molecular dynamics (MD) of 4,275 protein–compound pairs by combining a method to accelerate the MD simulations with the supercomputer Fugaku. Our spatiotemporal analysis of generated big MD data revealed universal features underlying molecular recognition and binding processes. This study expands our understanding of the concept of MD simulations from a technique to investigate the dynamic properties of individual protein–drug pairs to an approach to perform large-scale spatiotemporal analysis and compound screening. This study opens an avenue in biological research for subsequent drug discovery.

    DOI: 10.1093/pnasnexus/pgaf094

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  • DRD1-driven infantile dystonia: towards a mechanism-informed framework for GPCR receptoropathies Reviewed

    Gülsüm Kayhan, Ryosuke Tany, Reza Maroofian, Esra Serdaroğlu, Eon Kurumiya, Duy Phuoc Tran, Hideko Wakasugi-Masuho, Mirja Thomsen, Kamran Salayev, Rauan Kaiyrzhanov, Saadat Badalova, Ulviyya Guliyeva, Adel Kareem, Peter Bauer, Giovanni Zifarelli, Henry Houlden, Katja Lohmann, Akio Kitao, M Fatih Mulayim, Ikuo Masuho

    Brain   2026.4

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    Language:English   Publishing type:Research paper (scientific journal)  

    <jats:title>Abstract</jats:title>
    <jats:p>Despite remarkable advances in human genomics, most rare disorders remain undiagnosed, mechanistically obscure, and without effective treatments. In this study, we establish DRD1, encoding the dopamine D1 receptor (D1R), as a monogenic cause of an infantile-onset dystonia syndrome, for which pharmacological responsiveness may vary depending on the underlying molecular mechanism. Across three unrelated families, eight affected individuals exhibited generalised dystonia, axial hypotonia, and cognitive impairment and carried homozygous pathogenic missense DRD1 variants.</jats:p>
    <jats:p>Live-cell biosensor assays revealed that patient-derived DRD1 variants disrupt receptor integrity through mechanistically diverse failures, such as trafficking deficits and impaired agonist-induced activation—ultimately converging on a collapse of D1R-mediated signalling. In line with standard clinical practice and informed by these mechanistic insights, we initiated a trial of levodopa/carbidopa in two individuals in the index family with a partial-loss-of-function variant, which was associated with improvement in voluntary motor function and cognitive engagement. Moreover, in live-cell assays, we demonstrated that Mevidalen—a selective DRD1-positive allosteric modulator currently in clinical development—substantially improved signaling in patient-derived mutants in vitro, supporting a potential future mechanism-aligned therapeutic avenue.</jats:p>
    <jats:p>To broaden the clinical implications of our findings, we performed a structural interpretation of DRD1 variation in 807,162 individuals and identified 29 rare predicted deleterious missense variants in heterozygous carriers. These variants clustered within evolutionarily conserved transmembrane domains and signaling motifs, providing a basis for pathogenicity assignment and variant prioritization in clinical and research settings.</jats:p>
    <jats:p>Building on these insights, we developed a structure-informed pharmacological experimental framework that stratifies DRD1 variants according to molecular dysfunction and matches them with mechanistically aligned therapeutic strategies—namely, orthosteric agonists, pharmacological chaperones, allosteric modulators, and readthrough compounds. This in vitro approach enabled functional rescue of otherwise intractable variants, suggesting a potentially actionable molecular architecture across diverse genotypes, which remains to be tested clinically.</jats:p>
    <jats:p>Together, these findings identify biallelic DRD1 variants as a cause of infantile dystonia and support the potential for mechanism-informed therapeutic exploration, while emphasizing that clinical responsiveness may vary across individuals. More broadly, our integrated genomics-structure-pharmacology framework provides a proof-of-concept approach to functionally stratify G protein-coupled receptor (GPCR) variants, exemplified here by DRD1, and prioritise testable, mechanism-based therapeutic hypotheses for future evaluation.</jats:p>

    DOI: 10.1093/brain/awag128

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MISC

  • 最先端シミュレーションによる「弱い相互作用」の定量的予測

    北尾彰朗

    ファルマシア(Web)   61 ( 3 )   2025

Presentations

  • 結晶構造とMDシミュレーションで解き明かすナイーブ抗PEG抗体の認識戦略

    森 尚寛, 劉 一イ, 伊藤 悠世, 黒木 喜美子, 林 成一郎, 神田 大輔, 清水 太郎, 石田 竜弘, Roffler Steve R., 金子 美華, 加藤 幸成, 有森 貴夫, 寺本 岳大, 竹村 和浩, 石橋 賢汰, 片山 佳樹, 前仲 勝実, 北尾 彰朗, 森 健, 角田 佳充

    日本生化学会大会プログラム・講演要旨集  2025.11  (公社)日本生化学会

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    Event date: 2025.11

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  • GPR84のバイアス作動の解明

    鈴木翔大, TRAN Phuoc Duy, 西川幸希, 北尾彰朗, 藤吉好則

    日本蛋白質科学会年会(Web)  2025 

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  • 分子動力学シミュレーションによる天然変性タンパク質FUSのジンクフィンガードメインと天然変性領域による協調的な核酸結合機構の解明

    木島壮一朗, 北尾彰朗

    日本蛋白質科学会年会(Web)  2025 

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  • PaCS-MDによるアクトミオシンの結合解離予測

    尾川拓巳, Tran Phuoc Duy, 藤井高志, 難波啓一, 北尾彰朗

    第9回日本生物物理学会関東支部会  2020.3 

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    Event date: 2020.3

    Language:Japanese   Presentation type:Oral presentation (general)  

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  • In silico studies on the regulation mechanis Invited

    Akio Kitao

    2025.6 

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  • A deep dive into the nanoscale biological world with high-performance computing Invited

    The Post-graduate Research Day at The School of Computing Sciences, The University of East Anglia  2025.6 

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    Language:English   Presentation type:Public lecture, seminar, tutorial, course, or other speech  

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  • タンパク質の複合体形成・解離のダイナミクスとアロステリック効果 Invited

    北尾 彰朗

    物性研究所スパコン共同利用・CCMS合同研究会「機械学習と計算物性科学の未来」  2025.4 

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  • Specific and non-specific interactions of intrinsically disordered regions of proteins Invited

    Akio Kitao

    2025.3 

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  • 分⼦シミュレーションで観た細菌べん⽑固定⼦中のイオン透過 Invited

    北尾 彰朗

    cQUEST シンポジウム膜タンパク質内部のイオン透過を考える  2025.12 

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  • In silico investigation of the activation and inactivation mechanisms of G protein-coupled receptors Invited

    Akio Kitao

    63rd Annual Meeting of Biophysical Society of Japan  2025.9 

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  • Binding mechanisms and effects of intrinsically disordered regions of proteins Invited

    Akio Kitao

    TSRC Workshop on Protein Dynamics  2025.7 

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  • 最先端シミュレーションによる 物質共生に関わる相互作用の定量的予測 Invited

    北尾 彰朗

    「物質共生」取り纏めシンポジウム  2025.7 

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  • Transport mechanisms of ions and proteins across bacterial membranes Invited

    Akio Kitao

    Pacifichem 2025  2025.12 

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  • FlhB/FliPQR複合体のMDシミュレーション

    北尾彰朗

    2024年度べん毛研究交流会  2025.3 

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Works

  • PaCS-Toolkit

    Shinji Ikizawa, Tatsuki Hori, Tegar Nurwahyu Wijaya, Hiroshi Kono, Zhen Bai, Tatsuhiro Kimizono, Wenbo Lu, Duy Phuoc Tran, Akio Kitao

    2024.2

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  • eePaCS-MD (Edge expansion parallel cascade selection molecular dynamics)

    Kenichiro Takaba, Duy Phuoc Tran, Akio Kitao

    2020.6

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    Work type:Software  

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  • a/dPaCS-MD (association and dissociation PaCS-MD)

    Duy Phuoc Tran, Akio Kitao

    2020.3

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  • evERdock BAI (Machine-learning-guided selection of protein-protein complex structure)

    Kei Terayama, Ai Shinbu, Koji Tsuda, Kazuhiro Takemura, Akio Kitao

    2019.12

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    Work type:Software  

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  • dPaCS-MD/MSM

    Duy Phuoc Tran, Akio Kitao

    2019.1

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  • PaCS-MD/MSM

    Duy Phuoc Tran, Kazuhiro Takemura, Kazuo Kuwata, Akio Kitao

    2018.9

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  • ColDock (Concentrated Lingand Docking)

    Kazuhiro Takemura, Chika Sato, Akio Kitao

    2018.7

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  • evERdock (evaluation with the ER method of docking generated decoys)

    Kazuhiro Takemura, Nobuyuki Matubayasi, Akio Kitao

    2018.3

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  • CyClus (A fast, comprehensive cylindrical interface approximation clustering/reranking method for rigid-body protein-protein docking decoys)

    Satoshi Omori, Kazuhiro Takemura, Hiroaki Hata, Akio Kitao

    2017

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  • nt-PaCS-MD (nontargeted parallel cascade selection molecular dynamics)

    Ryuhei Harada, Akio Kitao

    2015.11

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  • MuSTAR MD ((Multi-scale sampling using temperature accelerated and replica exchange molecular dynamics)

    Yu Yamamori, Akio Kitao

    2013.10

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  • PaCS-MD (Parallel cascade selection molecular dynamics)

    Ryuhei Harada, Akio Kitao

    2013.7

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  • TRS (Transform and Relax Sampling)

    Akio Kitao

    2011.7

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  • MSFEL (Multi-Scale Free Energy Landscape calculation method by combination of coarse-grained and all-atom model)

    Ryuhei Harada, Akio Kitao

    2011.2

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  • Independent Subspace Analysis (ISA) with SJADE

    Shun Sakuraba, Yasumasa Joti, Akio Kitao

    2010

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  • PCA_NEST

    ee-Wei Yang, Eran Eyal, Ivet Bahar, Akio Kitao

    2009.3

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    Work type:Web Service  

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  • DTA app (Dihedral Transition Analysis application)

    Wataru Nishima, Guoying Qi, Steven Hayward, Akio Kitao

    2009.3

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  • DTA DATABASE (Dihedral Transition Analysis database)

    Wataru Nishima, Guoying Qi, Steven Hayward, Akio Kitao

    2009.3

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  • Transform and Relax Sampling

    Akio Kitao, Koji Yonekura, Saori Maki-Yonekura, Fadel A Samatey, Katsumi Imada, Keiichi Namba, Nobuhiro Go

    2006.3

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  • SCUBA (Simulation Code for hUge Biomolecular Assembly)

    Hisashi Ishida, Yasumasa Joto, Mariko Higuchi, Takuma Kano, Akio Kitao, Nobuhiro Go

    2004

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  • JAM Moldel (Jumping-Among-Minima Model)

    Akio Kitao, Steven Hayward, Nobuhiro Go

    1998.12

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Awards

  • Biophysics and Physicobiology Award for outstanding Paper

    2026.6   Biophysical Society of Japan   Binding free energy of protein/ligand complexes calculated using dissociation Parallel Cascade Selection Molecular Dynamics and Markov state model

    Hiroaki Hata, Duy Phuoc Tran, Mohamed Marzouk Sobeh, Akio Kitao

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    Award type:Honored in official journal of a scientific society, scientific journal  Country:Japan

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Research Projects

  • Generative design of protein molecular functions by molecular simulations

    Grant number:24H02259  2024.4 - 2029.3

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research  Grant-in-Aid for Transformative Research Areas (A)

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    Grant amount:\106730000 ( Direct Cost: \82100000 、 Indirect Cost:\24630000 )

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  • Molecular mechanisms of non-domain biopolymers investigated by highly efficient molecular simulation

    Grant number:24H01357  2024.4 - 2026.3

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research  Grant-in-Aid for Transformative Research Areas (A)

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    Grant amount:\9620000 ( Direct Cost: \7400000 、 Indirect Cost:\2220000 )

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  • Investigating molecular interactions of p53 regulated by post translation modifications and intrinsically disordered regions with advanced simulation

    Grant number:23K27138  2023.4 - 2027.3

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research  Grant-in-Aid for Scientific Research (B)

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    Grant amount:\18850000 ( Direct Cost: \14500000 、 Indirect Cost:\4350000 )

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  • Structural analysis of the recognition mechanism of diverse chemicals by taste receptors

    Grant number:23K27117  2023.4 - 2026.3

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research  Grant-in-Aid for Scientific Research (B)

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    Grant amount:\18720000 ( Direct Cost: \14400000 、 Indirect Cost:\4320000 )

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  • Quantitative prediction of the interactions involved in material symbiosis using advanced simulation

    Grant number:23H04058  2023.4 - 2025.3

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research  Grant-in-Aid for Transformative Research Areas (A)

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    Grant amount:\7800000 ( Direct Cost: \6000000 、 Indirect Cost:\1800000 )

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  • タンパク質のダイナミックス

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    Grant type:Competitive

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  • 蛋白質分子の設計

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    Grant type:Competitive

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  • タンパク質の複合体形成原理

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    Grant type:Competitive

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  • タンパク質の立体構造安定性

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    Grant type:Competitive

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Teaching Experience

  • 高大連携授業「先端科学技術入門」コンピュータで観るバイオ分子の働き

    2025.11 Institution:東京科学大学附属科学技術高等学校

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  • Bioinformatics 2

    2025.7 Institution:Institute of Science Tokyo

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  • Bioinformatics 3

    2025.7 Institution:Institute of Science Tokyo

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  • 化学特別講義1

    2025.6 - 2025.7 Institution:京都大学理学部

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  • Science Tokyo-Tsinghua Univ Joint graduate program. Molecular simulation of biomolecules: the basics and the applications

    2025.5 Institution:Tsinghua University

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  • 物理化学第三

    2019.9 Institution:東京工業大学生命理工学院

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  • Bioinformatics

    2019.3 Institution:Tokyo Institute of Technology, School of Life Science and Technology

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  • 基礎実験

    2018.4 Institution:東京工業大学生命理工学院

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  • Computational Biology

    2017.9 Institution:Tokyo Institute of Technology, School of Life Science and Technology

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  • 生物物理学II

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  • 生物物理学特論

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  • 物理学特別講義AXV

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  • 蛋白質立体構造解析学

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  • 全学自由研究ゼミナール

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  • 情報生命科学特別研究

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  • 情報生命科学演習

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  • 応用物理学第1

    Institution:慶應義塾大学

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  • 化学演習(熱力学・統計力学)

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  • 化学演習(量子・統計)

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  • 現代化学セミナー

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  • 量子化学研究特論

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  • 化学実験

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  • 計算機演習

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  • 生命と情報

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  • 物理学特別講義A

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  • 生体高分子動力学

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