Rchr
J-GLOBAL ID：201801007668388348   Update date: Jan. 21, 2026

Sugita Yuji

スギタ ユウジ | Sugita Yuji
Affiliation and department：
The University of Tokyo Graduate School of Science

About The University of Tokyo Graduate School of Science


Job title： Professor
Other affiliations (2)：
  • RIKEN  Pioneering Research Institute   Chief Scientist
  • RIKEN  Center for Computational Science   Team Principal
Homepage URL  (2)： https://tms.riken.jp/ ,  https://tms.riken.jp/en/
Research field  (3)： Basic physical chemistry ,  Computational science ,  Biophysics
Research keywords  (7)： Data-driven modeling ,  Quantum Chemistry ,  Machine Learning ,  Ion Pump ,  Biomolecular Dynamics in Cellular Environments ,  Enhanced Conformational Sampling Method ,  Molecular Dynamics Simulation
Research theme for competitive and other funds  (24)：
  • 2021 - 2026 Cross-scale data-driven modeling of biomolecular dynamics in the cells
  • 2021 - 2026 Cross-scale biology
  • 2019 - 2024 Multi-scale molecular dynamics simulation on biomolecular dynamics in crowded cellular environments
  • 2019 - 2020 「動的構造生命科学を拓く新発想測定技術」の成果取りまとめを目指した組織活動
  • 2016 - 2019 Development and application of a conformational search model to predict three-dimensional structural ensembles of glycans
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Papers (302)：
  • Shingo Ito, Chigusa Kobayashi, Kiyoshi Yagi, Yuji Sugita. Toward understanding whole enzymatic reaction cycles using multi-scale molecular simulations. Current Opinion in Structural Biology. 2025
  • Diego Ugarte La Torre, Yuji Sugita. CGBack: Diffusion Model for Backmapping Large-Scale and Complex Coarse-Grained Molecular Systems. Journal of Chemical Information and Modeling. 2025
  • Daisuke Matsuoka, Yuji Sugita, Takaharu Mori. An Empirical Biasing Force Constant to Minimize Overfitting in Cryo-EM Flexible Fitting Refinement. Journal of Chemical Information and Modeling. 2025
  • Masahiro Motohashi, Mao Oide, Chigusa Kobayashi, Jaewoon Jung, Eiro Muneyuki, Yuji Sugita. The distortion-push mechanism for the γ subunit rotation in F 1 -ATPase. Proceedings of the National Academy of Sciences. 2025
  • Tomoaki Yagi, Haeri Im, Song-Ho Chong, Yuji Sugita. Dynamic Shielding and Allosteric Modulation of Erythropoietin by Glycosylation. 2025
ｍore...
MISC (95)：
  • Chigusa KOBAYASHI, Yasuhiro MATSUNAGA, Jaewoon JUNG, Yuji SUGITA. Analyses of Structure Changes and Free Energy of Sarco/Endoplasmic Reticulum Ca<sup>2+</sup>-ATPase. Seibutsu Butsuri. 2022. 62. 5. 298-300
  • Hisham M. Dokainish, Suyong Re, Takaharu Mori, Chigusa Kobayashi, Jaewoon Jung, Yuji Sugita. Unraveling SARS-CoV-2 spike protein activation pathway reveals unprecedented cryptic pockets. BIOPHYSICAL JOURNAL. 2022. 121. 3. 457A-457A
  • Free-energy Calculation of Protein-Ligand Binding Using Molecular Dynamics Simulation Software "GENESIS". 2021. 40. 1. 22-28
  • ANDO Toshio, ITO Yutaka, SUGITA Yuji, NANGO Eriko, YASUNAGA Takuo, OKADA Yasushi, KANDA Genki N. New Technologies that Propel Biophysics. Seibutsu Butsuri. 2021. 61. 2. 111-118
  • 森貴治, 的場一晃, 野田展生, 杉田有治, 杉田有治, 杉田有治. オートファゴソーム形成に関与する膜タンパク質Atg9の膜中配向予測. 分子シミュレーション討論会講演要旨集. 2020. 34th (CD-ROM)
ｍore...
Books (1)：
  • 計算科学のためのHPC技術
    大阪大学出版会 2017 ISBN:9784872595864
Education (2)：
  • 1993 - 1998 Kyoto University Graduate School of Science Department of Chemistry
  • 1989 - 1993 Kyoto University Faculty of Science
Professional career (1)：
  • Ph. D. (Kyoto University)
Work history (6)：
  • 2025/10 - 現在 Graduate School of Science, The University of Tokyo Department of Physics Professor
  • 2012/04 - 現在 RIKEN Theoretical Molecular Science Laboratory Chief Scientist
  • 2007/04 - 2012/03 RIKEN Theoretical Biochemistry Laboratory Associate Chief Scientist
  • 2002/04 - 2007/03 The University of Tokyo Institute of Molecular and Cellular Biosciences Lecturer
  • 1998/09 - 2002/03 Institute for Molecular Science Research Associate
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Association Membership(s) (7)：
Biophysical Society ,  American Chemical Society ,  PROTEIN SCIENCE SOCIETY OF JAPAN ,  THE PHYSICAL SOCIETY OF JAPAN ,  THE MOLECULAR SIMULATION SOCIETY OF JAPAN ,  THE BIOPHYSICAL SOCIETY OF JAPAN ,  The Chemical Society of Japan
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