Sugita Yuji

スギタユウジ | Sugita Yuji

Affiliation and department：
Other affiliations (2)：

理化学研究所計算科学研究センターチームリーダー
理化学研究所生命機能科学研究センターチームリーダー

Homepage URL (1)： http://www.riken.jp/TMS2012/tms/ja/index.html

Research field (3)： Basic physical chemistry , Computational science , Biophysics

Research keywords (4)： 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

2015 - 2019 Support activities aimed at international network formation in the research area of dynamic structural life sciences

2014 - 2019 New measurement techniques for visualizing live protein molecules at work

2014 - 2019 Molecular dynamics simulations of protein complexes based on multi-resolution models

2014 - 2019 Molecular Science of NO Dyanmics in Biological System

2013 - 2017 Breakthrough on the high pressure biomolecule reaction with computational chemistry of the volume change

2013 - 2017 Structural analysis of asymmetrically branched glycans

2013 - 2016 Modeling and database development for complex glycans

2013 - 2014 Prediction of Protein-Glycan Structure Complex with Low Binding Affinity

2012 - 2014 タンパク質複合体形成の分子機構と自由エネルギー解析

2011 - 2012 Development of a new method for structural modeling of protein-membrane complexes

2010 - 2011 タンパク質複合体形成のダイナミクスと分子認識機構の解明

2003 - 2008 Molecular dynamics simulations on membrane transporting proteins

2002 - 2006 P型イオンポンプによる能動輪送機構の構造的解明

2003 - 2004 巨大膜蛋白質・脂質二重膜複合体の高精度分子動力学計算システムの開発

2002 - 2002 拡張アンサンブル法に基づく蛋白質フォールディング機構解析法の確立

2001 - 2002 アミノ酸変異による蛋白質の機能と安定性変化の物理化学的解明

2001 - 2001 新拡張アンサンブル法による蛋白質フォールディング機構の自由エネルギー解析

2000 - 2000 レプリカ交換法による蛋白質立体構造予測法の開発

1999 - 1999 新しい高精度のモデル内殻ポテンシャルの開発とそれらの応用

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Papers (274)：

Kazuki Watanabe, Qingci Zhao, Ryosuke Iwatsuki, Ryota Fukui, Weitong Ren, Yuji Sugita, Noritaka Nishida. Deciphering the Multi-state Conformational Equilibrium of HDM2 in the Regulation of p53 Binding: Perspectives from Molecular Dynamics Simulation and NMR Analysis. Journal of the American Chemical Society. 2024. 146. 14. 9790-9800
Ryo Nishihara, Hisham M. Dokainish, Yoshiki Kihara, Hiroki Ashiba, Yuji Sugita, Ryoji Kurita. Pseudo-Luciferase Activity of the SARS-CoV-2 Spike Protein for Cypridina Luciferin. ACS Central Science. 2024
Jaewoon Jung, Chigusa Kobayashi, Yuji Sugita. Acceleration of generalized replica exchange with solute tempering simulations of large biological systems on massively parallel supercomputer. Journal of Computational Chemistry. 2023
Cheng Tan, Ai Niitsu, Yuji Sugita. Highly Charged Proteins and Their Repulsive Interactions Antagonize Biomolecular Condensation. JACS Au. 2023. 3. 3. 834-848
Shingo Ito, Kiyoshi Yagi, Yuji Sugita. Allosteric regulation of beta-reaction stage I in tryptophan synthase upon the alpha-ligand binding. JOURNAL OF CHEMICAL PHYSICS. 2023. 158. 11

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MISC (93)：

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
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)
Yuji Sugita, Kento Kasahara, Hiraku Oshima, Isseki Yu, Grzegorz Nawrocki, Suyong Re, Michael Feig. Simulations of biomolecules in cellular crowded environments. JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS. 2019. 37. 51-52

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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)：

博士(理学) (京都大学)

Work history (5)：

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
1998/04 - 1998/08 RIKEN Postdoctoral Fellow

Association Membership(s) (6)：

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

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