SUGITA Yuji 杉田有治

… Alternative Names

杉田有冶スギタユウジ

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Researcher Number	80311190
Other IDs
External Links
Affiliation (Current)	2025: 国立研究開発法人理化学研究所, 開拓研究所, 主任研究員 2025: 国立研究開発法人理化学研究所, 計算科学研究センター, 副センター長
Affiliation (based on the past Project Information) *help	2018 – 2024: 国立研究開発法人理化学研究所, 開拓研究本部, 主任研究員 2016 – 2017: 国立研究開発法人理化学研究所, 主任研究員研究室等, 主任研究員 2015 – 2017: 国立研究開発法人理化学研究所, 杉田理論分子科学研究室, 主任研究員 2016: 理化学研究所, 杉田理論分子科学研究室, 主任研究員 2015: 国立研究開発法人理化学研究所, その他部局等, 主任研究員 … More 2014: 独立行政法人理化学研究所, その他部局等, その他 2012 – 2014: 独立行政法人理化学研究所, 杉田理論分子科学研究室, 主任研究員 2010 – 2011: 独立行政法人理化学研究所, 杉田理論生物化学研究室, 准主任研究員 2008: The Institute of Physical and Chemical Research, 杉田理論生物化学研究室, 准主任研究員 2007: The Institute of Physical and Chemical Research, 杉田理論生物化学研究室, 准主任研究員 2006: 独立行政法人理化学研究所, 中央研究所, 准主任研究員 2002 – 2006: 東京大学, 分子細胞生物学研究所, 講師 1999 – 2001: 岡崎国立共同研究機構, 分子科学研究所, 助手 Less
Review Section/Research Field	Principal Investigator Biological Sciences / Complex systems / Transformative Research Areas, Section (III) / Broad Section G / Life / Health / Medical informatics / Biophysics / Biophysics Except Principal Investigator Complex systems / Transformative Research Areas, Section (III) / Physical pharmacy / Life / Health / Medical informatics / Bio-related chemistry / Science and Engineering
Keywords	Principal Investigator 分子動力学 / 分子動力学法 / レプリカ交換法 / 拡張アンサンブル法 / 膜タンパク質 / マルチカノニカル法 / 細胞内環境 / 生体超分子複合体 / 自由エネルギー計算 / Tom20複合体 … More / 蛋白質間相互作用 / シミュレーション / 分子動力学計算 / 膜蛋白質 / データ駆動方モデリング / クロススケールモデリング / データ駆動モデリング / 分子ダイナミクス / クロススケールモデル / 分子動力学シミュレーション / マルチスケールシミュレーション / 蛋白質の構造柔軟性 / 酵素反応 / 蛋白質構造柔軟性 / マルチスケール / 機械学習 / 酵素反応解析 / 分子混雑環境 / スーパーコンピュータ / SAXS / NMR / 酵素反応ダイナミクス / 液液相分離 / 細胞内分子混雑環境 / マルチスケールモデル / 電子顕微鏡 / 構造解析法 / マルチスケール法 / 粗視化分子モデル / マルチスケール・マルチレゾリューション / フレキシブルフィッティグ / 一分子構造解析 / クライオ電子顕微鏡 / CMAP補正 / レプリカ交換分子動力学法 / レクチン / 糖鎖 / 低親和性複合体構造予測 / タンパク質ーリガンド認識 / レクチンOS9 / 分子認識 / 糖鎖複合体 / 分子シミュレーション / 有限温度String法 / 動的な複合体形成 / プレ配列認識機構 / 動的平衡 / 蛋白質/蛋白質相互作用 / 自由エネルギー / 分子認識機構 / 膜タンパク / イオン能動輸送 / プロトン化 / 生体膜 / 膜透過装置 / 物質輸送 / トランスロコン / イオンポンプ / 分子力場ポテンシャル / アミノ酸変異 / ヒトリゾチーム / 自由エネルギー摂動法 / C-peptide / Met-enkehpalin / 分子シミュレーション法 / 蛋白質折れ畳み問題 … More Except Principal Investigator N型糖鎖 / NMR / 動的構造 / 蛋白質 / X線結晶解析 / クライオ電電子線トモグラフィー / in-cell AFM / In-cell AFM / In-cell NMR / 超解像イメージング / クライオ電子線トモグラフィー / クロススケール / 新測定技術 / 構造生命科学 / DCIR2 / CLEC-2 / GnT-III / バイセクトGlcNAc / PIM / ZG16p / DCIR / PHA-E / Calsepa / 大量発現 / 気相電気泳動法 / βグルカン / Dectin-1 / 立体構造 / 分子動力学 / Ｘ線結晶構造解析 / 相互作用 / 分枝構造 / ダイナミクス / レクチン / 糖鎖 / 立体構造予測 / 衝突断面積 / イオンモビリティー質量スペクトル / レプリカ交換法 / 分子動力学計算 / 海外共同研究者受入 / 海外研究者招聘 / 海外講演者招聘 / 海外研究者受入 / 海外派遣 / 国際共同研究 / 環境科学 / 窒素循環 / 分子進化 / 温室効果ガス / 酵素反応 / 膜タンパク質 / 金属酵素 / 呼吸酵素 / 一酸化窒素還元酵素 / 脱窒 / 一酸化窒素 / Ｘ線結晶学 / X線結晶学 / ＡＦＭ / ＮＭＲ / 計算科学 / タンパク質 / 計算シミュレーション / 結晶解析 / ODMR / AFM / 測定技術 / ATPase / X線結晶 / イオンポンプ / 膜蛋白質 / 能動輸送 / 生物物理 / スピン軌道相互作用 / モデル内殻ポテンシャル / 分子軌道法 Less

Cross-scale biology
- Principal Investigator
  
  吉川雅英
- Project Period (FY)
  2021 – 2025
- Research Category
  
  Grant-in-Aid for Transformative Research Areas (A)
- Review Section
  
  Transformative Research Areas, Section (III)
- Research Institution
  The University of Tokyo
Cross-scale data-driven modeling of biomolecular dynamics in the cellsPrincipal Investigator
- Principal Investigator
  
  杉田有治
- Project Period (FY)
  2021 – 2025
- Research Category
  
  Grant-in-Aid for Transformative Research Areas (A)
- Review Section
  
  Transformative Research Areas, Section (III)
- Research Institution
  Institute of Physical and Chemical Research
「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
- Principal Investigator
  
  神田大輔
- Project Period (FY)
  2019
- Research Category
  
  Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)
- Review Section
  
  Complex systems
- Research Institution
  Kyushu University
Multi-scale molecular dynamics simulation on biomolecular dynamics in crowded cellular environmentsPrincipal Investigator
- Principal Investigator
  
  Sugita Yuji
- Project Period (FY)
  2019 – 2023
- Research Category
  
  Grant-in-Aid for Scientific Research (S)
- Review Section
  
  Broad Section G
- Research Institution
  Institute of Physical and Chemical Research
Support activities aimed at international network formation in the research area of dynamic structural life sciences
- Principal Investigator
  
  Kohda Daisuke
- Project Period (FY)
  2015 – 2018
- Research Category
  
  Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)
- Review Section
  
  Complex systems
- Research Institution
  Kyushu University
New measurement techniques for visualizing live protein molecules at work
- Principal Investigator
  
  Kohda Daisuke
- Project Period (FY)
  2014 – 2018
- Research Category
  
  Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)
- Review Section
  
  Complex systems
- Research Institution
  Kyushu University
Molecular dynamics simulations of protein complexes based on multi-resolution modelsPrincipal Investigator
- Principal Investigator
  
  Sugita Yuji
- Project Period (FY)
  2014 – 2018
- Research Category
  
  Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)
- Review Section
  
  Complex systems
- Research Institution
  Institute of Physical and Chemical Research
Molecular Science of NO Dyanmics in Biological System
- Principal Investigator
  
  Shiro Yoshitsugu
- Project Period (FY)
  2014 – 2018
- Research Category
  
  Grant-in-Aid for Scientific Research (S)
- Research Field
  
  Bio-related chemistry
- Research Institution
  University of Hyogo
  Institute of Physical and Chemical Research
Prediction of Protein-Glycan Structure Complex with Low Binding AffinityPrincipal Investigator
- Principal Investigator
  
  SUGITA Yuji
- Project Period (FY)
  2013
- Research Category
  
  Grant-in-Aid for Challenging Exploratory Research
- Research Field
  
  Life / Health / Medical informatics
- Research Institution
  Institute of Physical and Chemical Research
Modeling and database development for complex glycans
- Principal Investigator
  
  Re Suyong
- Project Period (FY)
  2013 – 2015
- Research Category
  
  Grant-in-Aid for Scientific Research (C)
- Research Field
  
  Life / Health / Medical informatics
- Research Institution
  Institute of Physical and Chemical Research
Structural analysis of asymmetrically branched glycans
- Principal Investigator
  
  Yamaguchi Yoshiki
- Project Period (FY)
  2013 – 2016
- Research Category
  
  Grant-in-Aid for Scientific Research (C)
- Research Field
  
  Physical pharmacy
- Research Institution
  Institute of Physical and Chemical Research
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Principal Investigator
- Principal Investigator
  
  杉田有治
- Project Period (FY)
  2012 – 2013
- Research Category
  
  Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)
- Review Section
  
  Complex systems
- Research Institution
  The Institute of Physical and Chemical Research
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Principal Investigator
- Principal Investigator
  
  杉田有治
- Project Period (FY)
  2010 – 2011
- Research Category
  
  Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)
- Review Section
  
  Complex systems
- Research Institution
  The Institute of Physical and Chemical Research
Molecular dynamics simulations on membrane transporting proteinsPrincipal Investigator
- Principal Investigator
  
  SUGITA Yuji
- Project Period (FY)
  2003 – 2008
- Research Category
  
  Grant-in-Aid for Scientific Research on Priority Areas
- Review Section
  
  Biological Sciences
- Research Institution
  The Institute of Physical and Chemical Research
  The University of Tokyo
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Principal Investigator
- Principal Investigator
  
  杉田有治
- Project Period (FY)
  2003 – 2004
- Research Category
  
  Grant-in-Aid for Young Scientists (B)
- Research Field
  
  Biophysics
- Research Institution
  The University of Tokyo
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Principal Investigator
- Principal Investigator
  
  杉田有治
- Project Period (FY)
  2002
- Research Category
  
  Grant-in-Aid for Scientific Research on Priority Areas
- Review Section
  
  Biological Sciences
- Research Institution
  The University of Tokyo
P型イオンポンプによる能動輪送機構の構造的解明
- Principal Investigator
  
  豊島近
- Project Period (FY)
  2002 – 2006
- Research Category
  
  Grant-in-Aid for Creative Scientific Research
- Research Institution
  The University of Tokyo
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Principal Investigator
- Principal Investigator
  
  杉田有治
- Project Period (FY)
  2001
- Research Category
  
  Grant-in-Aid for Scientific Research on Priority Areas (C)
- Review Section
  
  Biological Sciences
- Research Institution
  Okazaki National Research Institutes
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Principal Investigator
- Principal Investigator
  
  杉田有治
- Project Period (FY)
  2001 – 2002
- Research Category
  
  Grant-in-Aid for Young Scientists (B)
- Research Field
  
  Biophysics
- Research Institution
  The University of Tokyo
  Okazaki National Research Institutes
レプリカ交換法による蛋白質立体構造予測法の開発Principal Investigator
- Principal Investigator
  
  杉田有治
- Project Period (FY)
  2000
- Research Category
  
  Grant-in-Aid for Scientific Research on Priority Areas (C)
- Review Section
  
  Biological Sciences
- Research Institution
  Okazaki National Research Institutes
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
- Principal Investigator
  
  三好永作
- Project Period (FY)
  1999
- Research Category
  
  Grant-in-Aid for Scientific Research on Priority Areas (A)
- Review Section
  
  Science and Engineering
- Research Institution
  Okazaki National Research Institutes

[Book] In-cell NMR Spectroscopy: From Molecular Sciences to Cell Biology2019
- Author(s)
  Yuji Sugita, Michael Feig
- Total Pages
  305
- Publisher
  Royal Society of Chemistry
- ISBN
  9781788012171
- Data Source
  KAKENHI-PROJECT-19H05645
[Book] Biomolecular Simulation: Methods and Protocols2019
- Author(s)
  Yuji Sugita, Motoshi Kamiya, Hiraku Oshima, Suyong Re
- Total Pages
  578
- Publisher
  Springer
- ISBN
  9781493996070
- Data Source
  KAKENHI-PROJECT-19H05645
[Book] Rugged Free Energy Landscapes2008
- Author(s)
  Y. Sugita, et al.
- Total Pages
  412
- Publisher
  Springer
- Data Source
  KAKENHI-PROJECT-15083201
[Journal Article] Free-energy landscapes of transmembrane homodimers by bias-exchange adaptively biased molecular dynamics2024
- Author(s)
  Ito Shingo、Sugita Yuji
- Journal Title
  
  Biophysical Chemistry
  
  Volume: 307 Pages: 107190-107190
- DOI
  10.1016/j.bpc.2024.107190
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PLANNED-21H05249, KAKENHI-PROJECT-19H05645
[Journal Article] SPANA: Spatial decomposition analysis for cellular-scale molecular dynamics simulations2024
- Author(s)
  Isseki Yu, Takaharu Mori, Daisuke Matsuoka, Donatas Surblys, Yuji Sugita1
- Journal Title
  
  Journal of Computational Chemistry
  
  Volume: 45 Issue: 8 Pages: 498-505
- DOI
  10.1002/jcc.27260
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-19K05389, KAKENHI-PLANNED-21H05249, KAKENHI-PLANNED-21H05157, KAKENHI-PROJECT-19H05645
[Journal Article] GENESIS CGDYN: large-scale coarse-grained MD simulation with dynamic load balancing for heterogeneous biomolecular systems2024
- Author(s)
  Jung Jaewoon、Tan Cheng、Sugita Yuji
- Journal Title
  
  Nature Communications
  
  Volume: 15 Issue: 1 Pages: 3370-3370
- DOI
  10.1038/s41467-024-47654-1
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PLANNED-21H05249, KAKENHI-PLANNED-21H05282, KAKENHI-PROJECT-19H05645
[Journal Article] Development of Hidden Markov Modeling of Molecular Orientations and Structures from High-Speed Atomic Force Microscopy Time-Series Images2023
- Author(s)
  Tomonori Ogane, Daisuke Noshiro, Toshio Ando, Atsuko Yamashita, Yuji Sugita, Yasuhiro Matsunaga
- Journal Title
  
  PLoS Comp. Biol.
  
  Volume: 18 Issue: 12 Pages: e1010384-e1010384
- DOI
  10.1371/journal.pcbi.1010384
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-19H05645, KAKENHI-PROJECT-22H00405, KAKENHI-PROJECT-20H03195, KAKENHI-PROJECT-20K21380
[Journal Article] Acceleration of generalized replica exchange with solute tempering simulations of large biological systems on massively parallel supercomputer2023
- Author(s)
  Jung Jaewoon、Kobayashi Chigusa、Sugita Yuji
- Journal Title
  
  Journal of Computational Chemistry
  
  Volume: - Issue: 20 Pages: 1740-1749
- DOI
  10.1002/jcc.27124
- Peer Reviewed
- Data Source
  KAKENHI-PLANNED-21H05282, KAKENHI-PLANNED-21H05249, KAKENHI-PROJECT-19H05645
[Journal Article] Extension of the iSoLF implicit-solvent coarse-grained model for multicomponent lipid bilayers2023
- Author(s)
  Ugarte La Torre Diego、Takada Shoji、Sugita Yuji
- Journal Title
  
  The Journal of Chemical Physics
  
  Volume: 159 Issue: 7 Pages: 75101-75101
- DOI
  10.1063/5.0160417
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PLANNED-21H05249, KAKENHI-PROJECT-19H05645
[Journal Article] Highly charged proteins and their repulsive interactions antagonize biomolecular condensation2023
- Author(s)
  Cheng Tan, Ai Niitsu, Yuji Sugita
- Journal Title
  
  JACS Au
  
  Volume: 3 Issue: 3 Pages: 834-848
- DOI
  10.1021/jacsau.2c00646
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PLANNED-21H05249, KAKENHI-PLANNED-21H05282, KAKENHI-PROJECT-19H05645, KAKENHI-PROJECT-21J40162
[Journal Article] Allosteric regulation of ホイ-reaction stage I in tryptophan synthase upon the ホア-ligand binding2023
- Author(s)
  Shingo Ito, Kiyoshi Yagi, Yuji Sugita
- Journal Title
  
  J. Chem. Phys.
  
  Volume: 158 Issue: 11 Pages: 115101-115101
- DOI
  10.1063/5.0134117
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-19H05645, KAKENHI-PROJECT-20H02701, KAKENHI-PUBLICLY-22H04761
[Journal Article] Protein Folding Intermediates on the Dimensionality Reduced Landscape with UMAP and Native Contact Likelihood2022
- Author(s)
  Mao Oide, Yuji Sugita
- Journal Title
  
  J. Chem. Phys.
  
  Volume: 157 Issue: 7 Pages: 75101-75101
- DOI
  10.1063/5.0099094
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PLANNED-21H05249, KAKENHI-PROJECT-19H05645
[Journal Article] Protein assembly and crowding simulations2022
- Author(s)
  Lim Heo, Yuji Sugita, Michael Feig
- Journal Title
  
  Curr. Opin. Struct. Biol.
  
  Volume: 73 Pages: 102340-102340
- DOI
  10.1016/j.sbi.2022.102340
- Peer Reviewed / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-21H05249, KAKENHI-PROJECT-19H05645
[Journal Article] Analyses of Structure Changes and Free Energy of Sarco/Endoplasmic Reticulum Ca<sup>2+</sup>-ATPase2022
- Author(s)
  小林千草, 松永康佑, Jaewoon Jung, 杉田有治
- Journal Title
  
  Seibutsu Butsuri
  
  Volume: 62 Issue: 5 Pages: 298-300
- DOI
  10.2142/biophys.62.298
- ISSN
  0582-4052, 1347-4219
- Language
  Japanese
- Open Access
- Data Source
  KAKENHI-PLANNED-21H05249
[Journal Article] Yuxia Zhang, Chigusa Kobayashi, Xiaohan Cai, Satoshi Watanabe, Akihisa Tsutsumi, Masahide Kikkawa, Yuji Sugita, Kenji Inaba2022
- Author(s)
  Yuxia Zhang, Chigusa Kobayashi, Xiaohan Cai, Satoshi Watanabe, Akihisa Tsutsumi, Masahide Kikkawa, Yuji Sugita, Kenji Inaba
- Journal Title
  
  Cell reports
  
  Volume: 41 Issue: 10 Pages: 111760-111760
- DOI
  10.1016/j.celrep.2022.111760
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-21H05249, KAKENHI-PLANNED-21H05253, KAKENHI-PROJECT-19H05645, KAKENHI-PROJECT-21H04758
[Journal Article] Practical Protocols for Efficient Sampling of Kinase-Inhibitor Binding Pathways Using Two-Dimensional Replica-Exchange Molecular Dynamics2022
- Author(s)
  Shinobu Ai、Re Suyong、Sugita Yuji
- Journal Title
  
  Frontiers in Molecular Biosciences
  
  Volume: 9 Pages: 878830-878830
- DOI
  10.3389/fmolb.2022.878830
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-19K12229, KAKENHI-PLANNED-21H05249, KAKENHI-PROJECT-19H05645
[Journal Article] Implementation of residue-level coarse-grained models I GENESIS for large-scale molecular dynamics simulations2022
- Author(s)
  Cheng Tan, Jaewoon Jung, Chigusa Kobayashi, Diego Ugarte, Shoji Takada, Yuji Sugita
- Journal Title
  
  PLoS Comp. Biol.
  
  Volume: 18 Issue: 4 Pages: e1009578-e1009578
- DOI
  10.1371/journal.pcbi.1009578
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PLANNED-21H05249, KAKENHI-PLANNED-21H05282, KAKENHI-PROJECT-19H05645
[Journal Article] Structural Effects of Spike Protein D614G Mutation in SARS-CoV-22022
- Author(s)
  Hisham M. Dokainish, Yuji Sugita
- Journal Title
  
  Biophys. J.
  
  Volume: 122 Issue: 14 Pages: 1-11
- DOI
  10.1016/j.bpj.2022.11.025
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PLANNED-21H05249, KAKENHI-PROJECT-19H05645
[Journal Article] Modified protein-water interactions in CHARMM36m for thermodynamics and kinetics of proteins in dilute and crowded solutions2022
- Author(s)
  Daiki Matsubara, Kento Kasahara, Hisham Dokainish, Hiraku Oshima, Yuji Sugita
- Journal Title
  
  Molecules
  
  Volume: 27 Issue: 17 Pages: 5726-5726
- DOI
  10.3390/molecules27175726
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PLANNED-21H05249, KAKENHI-PROJECT-19H05645
[Journal Article] Weight average approaches for predicting dynamical properties of biomolecules2022
- Author(s)
  Yagi Kiyoshi、Re Suyong、Mori Takaharu、Sugita Yuji
- Journal Title
  
  Current Opinion in Structural Biology
  
  Volume: 72 Pages: 88-94
- DOI
  10.1016/j.sbi.2021.08.008
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-19K06532, KAKENHI-PROJECT-19K12229, KAKENHI-PLANNED-21H05157, KAKENHI-PROJECT-20H02701, KAKENHI-PROJECT-19H05645
[Journal Article] Computational analysis on the allostery of tryptophan synthase: relationship between α/β-ligand binding and distal domain closure2022
- Author(s)
  Shingo Ito, Kiyoshi Yagi, Yuji Sugita
- Journal Title
  
  J. Phys. Chem. B
  
  Volume: 126 Issue: 17 Pages: 3300-3308
- DOI
  10.1021/acs.jpcb.2c01556
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PLANNED-21H05249, KAKENHI-PROJECT-19H05645, KAKENHI-PROJECT-20H02701
[Journal Article] Use of multistate Bennett acceptance ratio method for free-energy calculations from enhanced sampling and free-energy perturbation2022
- Author(s)
  Matsunaga Yasuhiro、Kamiya Motoshi、Oshima Hiraku、Jung Jaewoon、Ito Shingo、Sugita Yuji
- Journal Title
  
  Biophysical Reviews
  
  Volume: 14 Issue: 6 Pages: 1503-1512
- DOI
  10.1007/s12551-022-01030-9
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PLANNED-21H05282, KAKENHI-PROJECT-19H05645, KAKENHI-PROJECT-20K21380
[Journal Article] Modified Hamiltonian in FEP Calculations for Reducing the Computational Cost of Electrostatic Interactions2022
- Author(s)
  Hiraku Oshima, Yuji Sugita
- Journal Title
  
  J. Chem. Inf. Model.
  
  Volume: 62 Issue: 11 Pages: 2846-2856
- DOI
  10.1021/acs.jcim.1c01532
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-19H05645
[Journal Article] Towards de novo design of transmembrane α-helical assemblies using structural modelling and molecular dynamics simulation2022
- Author(s)
  Ai Niitsu, Yuji Sugita
- Journal Title
  
  Biophys. Rev.
  
  Volume: 14 Issue: 5 Pages: 1-10
- DOI
  10.1039/d2cp03972a
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PLANNED-21H05249, KAKENHI-PUBLICLY-22H05438, KAKENHI-PROJECT-19H05645, KAKENHI-PROJECT-21J40162, KAKENHI-PUBLICLY-21H00412
[Journal Article] The inherent flexibility of receptor binding domains in SARS-CoV-2 spike protein2022
- Author(s)
  Dokainish Hisham M、Re Suyong、Mori Takaharu、Kobayashi Chigusa、Jung Jaewoon、Sugita Yuji
- Journal Title
  
  eLife
  
  Volume: 11
- DOI
  10.7554/elife.75720
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-19K06532, KAKENHI-PROJECT-19K12229, KAKENHI-PROJECT-20K15737, KAKENHI-PLANNED-21H05249, KAKENHI-PLANNED-21H05157, KAKENHI-PROJECT-19H05645
[Journal Article] Exploring the Minimum-Energy Pathways and Free-Energy Profiles of Enzymatic Reactions with QM/MM Calculations2021
- Author(s)
  Yagi Kiyoshi、Ito Shingo、Sugita Yuji
- Journal Title
  
  The Journal of Physical Chemistry B
  
  Volume: 125 Issue: 18 Pages: 4701-4713
- DOI
  10.1021/acs.jpcb.1c01862
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-20H02701, KAKENHI-PROJECT-19H05645
[Journal Article] Efficient Flexible Fitting Refinement with Automatic Error Fixing for De Novo Structure Modeling from Cryo-EM Density Maps2021
- Author(s)
  Mori Takaharu、Terashi Genki、Matsuoka Daisuke、Kihara Daisuke、Sugita Yuji
- Journal Title
  
  Journal of Chemical Information and Modeling
  
  Volume: 61 Issue: 7 Pages: 3516-3528
- DOI
  10.1021/acs.jcim.1c00230
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-19K06532, KAKENHI-PROJECT-19H05645
[Journal Article] Structural and energetic analysis of metastable intermediate states in the E1P-E2P transition of Ca2+-ATPase2021
- Author(s)
  C. Kobayashi, Y. Matsunaga, J. Jung, Y. Sugita
- Journal Title
  
  Proceeding of the National Academy of Sciences of the United States of America
  
  Volume: 118 Issue: 40
- DOI
  10.1073/pnas.2105507118
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-20K21380, KAKENHI-PROJECT-19H05645
[Journal Article] Coarse-Grained Modeling of Multiple Pathways in Conformational Transitions of Multi-Domain Proteins2021
- Author(s)
  A. Shinobu, C. Kobayashi, Y. Matsunaga, and Y. Sugita
- Journal Title
  
  Journal of Chemical Information and Modeling
  
  Volume: 61 Issue: 5 Pages: 2427-2443
- DOI
  10.1021/acs.jcim.1c00286
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-20K21380, KAKENHI-PROJECT-19H05645
[Journal Article] Molecular Basis for Two Stereoselective Diels-Alderases that Produce Decalin Skeletons2021
- Author(s)
  Fujiyama Keisuke、Kato Naoki、Re Suyong、Kinugasa Kiyomi、Watanabe Kohei、Takita Ryo、Nogawa Toshihiko、Hino Tomoya、Osada Hiroyuki、Sugita Yuji、Takahashi Shunji、Nagano Shingo
- Journal Title
  
  Angewandte Chemie International Edition
  
  Volume: 60 Issue: 41 Pages: 22401-22410
- DOI
  10.1002/anie.202106186
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-19K06992, KAKENHI-PROJECT-19K12229, KAKENHI-PROJECT-20K15273, KAKENHI-PLANNED-19H05780, KAKENHI-PUBLICLY-20H05445, KAKENHI-PROJECT-20K05858, KAKENHI-PROJECT-20K05872, KAKENHI-PROJECT-21K19099, KAKENHI-PROJECT-19H05645, KAKENHI-PROJECT-20H00416, KAKENHI-PLANNED-17H06412
[Journal Article] Anharmonic Vibrational Calculations Based on Group-Localized Coordinates: Applications to Internal Water Molecules in Bacteriorhodopsin2021
- Author(s)
  Yagi Kiyoshi、Sugita Yuji
- Journal Title
  
  Journal of Chemical Theory and Computation
  
  Volume: 17 Issue: 8 Pages: 5007-5020
- DOI
  10.1021/acs.jctc.1c00060
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-20H02701, KAKENHI-PROJECT-19H05645
[Journal Article] Multi-Scale Flexible Fitting of Proteins to Cryo-EM Density Maps at Medium Resolution2021
- Author(s)
  Kulik Marta、Mori Takaharu、Sugita Yuji
- Journal Title
  
  Frontiers in Molecular Biosciences
  
  Volume: 8
- DOI
  10.3389/fmolb.2021.631854
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-19H05645
[Journal Article] Reduced Efficacy of a Src Kinase Inhibitor in Crowded Protein Solution.2021
- Author(s)
  Kento Kasahara, Suyong Re, Grzegorz Nawrocki, Hiraku Oshima, Chiemi Mishima-Tsumagari, Yukako Miyata-Yabuki, Mutsuko Kukimoto-Niino, Isseki Yu, Mikako Shirouzu, Michael Feig, Yuji Sugita
- Journal Title
  
  Nature Communications
  
  Volume: 12 Issue: 1 Pages: 4099-4099
- DOI
  10.1038/s41467-021-24349-5
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-19H05645
[Journal Article] Elucidation of interactions regulating conformational stability and dynamics of SARS-CoV-2 S-protein2021
- Author(s)
  Mori Takaharu、Jung Jaewoon、Kobayashi Chigusa、Dokainish Hisham M.、Re Suyong、Sugita Yuji
- Journal Title
  
  Biophysical Journal
  
  Volume: 120 Issue: 6 Pages: 1060-1071
- DOI
  10.1016/j.bpj.2021.01.012
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-19K06532, KAKENHI-PROJECT-19K12229, KAKENHI-PROJECT-19H05645
[Journal Article] Optimized Hydrogen Mass Repartitioning Scheme Combined with Accurate Temperature/Pressure Evaluations for Thermodynamic and Kinetic Properties of Biological Systems2021
- Author(s)
  Jaewoon Jung, Kento Kasahara, Chigusa Kobayashi, Hiraku Oshima, Takaharu Mori, and Yuji Sugita
- Journal Title
  
  J. Chem. Theory Comput.
  
  Volume: 17 Issue: 8 Pages: 5312-5321
- DOI
  10.1021/acs.jctc.1c00185
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-19H05645
[Journal Article] Unraveling the Coupling between Conformational Changes and Ligand Binding in Ribose Binding Protein Using Multiscale Molecular Dynamics and Free-Energy Calculations2021
- Author(s)
  Ren Weitong、Dokainish Hisham M.、Shinobu Ai、Oshima Hiraku、Sugita Yuji
- Journal Title
  
  The Journal of Physical Chemistry B
  
  Volume: 125 Issue: 11 Pages: 2898-2909
- DOI
  10.1021/acs.jpcb.0c11600
- Peer Reviewed / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-19H05645, KAKENHI-PROJECT-20K15737
[Journal Article] Exploring Large Domain Motions in Proteins Using Atomistic Molecular Dynamics with Enhanced Conformational Sampling2020
- Author(s)
  Dokainish Hisham M.、Sugita Yuji
- Journal Title
  
  International Journal of Molecular Sciences
  
  Volume: 22 Issue: 1 Pages: 270-270
- DOI
  10.3390/ijms22010270
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-19H05645, KAKENHI-PROJECT-20K15737
[Journal Article] Free Energy Analysis of a Conformational Change of Heme ABC Transporter BhuUV-T2020
- Author(s)
  Tamura Koichi、Sugita Yuji
- Journal Title
  
  The Journal of Physical Chemistry Letters
  
  Volume: 11 Issue: 8 Pages: 2824-2829
- DOI
  10.1021/acs.jpclett.0c00547
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-19H05645
[Journal Article] Group-based evaluation of temperature and pressure for molecular dynamics simulation with a large time step2020
- Author(s)
  Jung Jaewoon、Sugita Yuji
- Journal Title
  
  The Journal of Chemical Physics
  
  Volume: 153 Issue: 23 Pages: 234115-234115
- DOI
  10.1063/5.0027873
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-19H05645
[Journal Article] Use of single-molecule time-series data for refining conformational dynamics in molecular simulations2020
- Author(s)
  Matsunaga Yasuhiro、Sugita Yuji
- Journal Title
  
  Current Opinion in Structural Biology
  
  Volume: 61 Pages: 153-159
- DOI
  10.1016/j.sbi.2019.12.022
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-19H05645
[Journal Article] Prediction of Protein-Ligand Binding Pose and Affinity Using the gREST+FEP Method2020
- Author(s)
  Oshima Hiraku、Re Suyong、Sugita Yuji
- Journal Title
  
  Journal of Chemical Information and Modeling
  
  Volume: 60 Issue: 11 Pages: 5382-5394
- DOI
  10.1021/acs.jcim.0c00338
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-19K12229, KAKENHI-PROJECT-19H05645
[Journal Article] A singularity-free torsion angle potential for coarse-grained molecular dynamics simulations2020
- Author(s)
  Tan Cheng、Jung Jaewoon、Kobayashi Chigusa、Sugita Yuji
- Journal Title
  
  The Journal of Chemical Physics
  
  Volume: 153 Issue: 4 Pages: 044110-044110
- DOI
  10.1063/5.0013089
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-19H05645
[Journal Article] New parallel computing algorithm of molecular dynamics for extremely huge scale biological systems2020
- Author(s)
  Jung Jaewoon、Kobayashi Chigusa、Kasahara Kento、Tan Cheng、Kuroda Akiyoshi、Minami Kazuo、Ishiduki Shigeru、Nishiki Tatsuo、Inoue Hikaru、Ishikawa Yutaka、Feig Michael、Sugita Yuji
- Journal Title
  
  Journal of Computational Chemistry
  
  Volume: 42 Issue: 4 Pages: 231-241
- DOI
  10.1002/jcc.26450
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-19H05645
[Journal Article] Atg9 is a lipid scramblase that mediates autophagosomal membrane expansion2020
- Author(s)
  Matoba Kazuaki、Kotani Tetsuya、Tsutsumi Akihisa、Tsuji Takuma、Mori Takaharu、Noshiro Daisuke、Sugita Yuji、Nomura Norimichi、Iwata So、Ohsumi Yoshinori、Fujimoto Toyoshi、Nakatogawa Hitoshi、Kikkawa Masahide、Noda Nobuo N.
- Journal Title
  
  Nature Structural & Molecular Biology
  
  Volume: 27 Issue: 12 Pages: 1185-1193
- DOI
  10.1038/s41594-020-00518-w
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-19K06532, KAKENHI-PROJECT-19K07265, KAKENHI-PROJECT-19K16071, KAKENHI-PROJECT-19K16344, KAKENHI-PLANNED-19H05707, KAKENHI-PUBLICLY-20H05339, KAKENHI-PROJECT-16H06375, KAKENHI-PROJECT-19H05645, KAKENHI-PROJECT-18H03989, KAKENHI-PROJECT-18H04023, KAKENHI-PROJECT-19H00923, KAKENHI-PROJECT-18K05334, KAKENHI-PROJECT-18K06097, KAKENHI-PLANNED-19H05708, KAKENHI-PLANNED-19H05777
[Journal Article] CHARMM-GUI Free Energy Calculator for Absolute and Relative Ligand Solvation and Binding Free Energy Simulations2020
- Author(s)
  Kim Seonghoon、Oshima Hiraku、Zhang Han、Kern Nathan R.、Re Suyong、Lee Jumin、Roux Benoit、Sugita Yuji、Jiang Wei、Im Wonpil
- Journal Title
  
  Journal of Chemical Theory and Computation
  
  Volume: 16 Issue: 11 Pages: 7207-7218
- DOI
  10.1021/acs.jctc.0c00884
- Peer Reviewed / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-19K12229, KAKENHI-PROJECT-19H05645
[Journal Article] Acceleration of cryo-EM Flexible Fitting for Large Biomolecular Systems by Efficient Space Partitioning2019
- Author(s)
  Mori Takaharu、Kulik Marta、Miyashita Osamu、Jung Jaewoon、Tama Florence、Sugita Yuji
- Journal Title
  
  Structure
  
  Volume: 27 Issue: 1 Pages: 161-174.e3
- DOI
  10.1016/j.str.2018.09.004
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-16K07286, KAKENHI-PROJECT-17K07305, KAKENHI-PLANNED-26119006
[Journal Article] Refining Markov state models for conformational dynamics using ensemble-averaged data and time-series trajectories2018
- Author(s)
  Matsunaga Y.、Sugita Y.
- Journal Title
  
  The Journal of Chemical Physics
  
  Volume: 148 Issue: 24 Pages: 241731-241731
- DOI
  10.1063/1.5019750
- Peer Reviewed
- Data Source
  KAKENHI-PLANNED-26119006
[Journal Article] Flexible selection of the solute region in replica exchange with solute tempering: Application to protein-folding simulations2018
- Author(s)
  Kamiya Motoshi、Sugita Yuji
- Journal Title
  
  The Journal of Chemical Physics
  
  Volume: 149 Issue: 7 Pages: 072304-072304
- DOI
  10.1063/1.5016222
- Peer Reviewed
- Data Source
  KAKENHI-PLANNED-26119006
[Journal Article] Optimal Temperature Evaluation in Molecular Dynamics Simulations with a Large Time Step2018
- Author(s)
  Jung Jaewoon、Kobayashi Chigusa、Sugita Yuji
- Journal Title
  
  Journal of Chemical Theory and Computation
  
  Volume: 15 Issue: 1 Pages: 84-94
- DOI
  10.1021/acs.jctc.8b00874
- Peer Reviewed
- Data Source
  KAKENHI-PLANNED-26119006, KAKENHI-PROJECT-16K05526
[Journal Article] Linking time-series of single-molecule experiments with molecular dynamics simulations by machine learning2018
- Author(s)
  Matsunaga Yasuhiro、Sugita Yuji
- Journal Title
  
  eLife
  
  Volume: 7 Pages: 32668-32668
- DOI
  10.7554/elife.32668
- Peer Reviewed
- Data Source
  KAKENHI-PLANNED-26119006
[Journal Article] Flexible fitting to cryo-EM density map using ensemble molecular dynamics simulations2017
- Author(s)
  Miyashita O, Kobayashi C, Mori T, Sugita Y, Tama F
- Journal Title
  
  J. Comp. Chem
  
  Volume: 38 Issue: 16 Pages: 1447-1461
- DOI
  10.1002/jcc.24785
- Peer Reviewed / Acknowledgement Compliant
- Data Source
  KAKENHI-PLANNED-26119006, KAKENHI-PROJECT-16K07286
[Journal Article] Neural Network and Nearest Neighbor Algorithms for Enhancing Sampling of Molecular Dynamics2017
- Author(s)
  Raimondas Galvelis, and Yuji Sugita
- Journal Title
  
  J. Chem. Theor. Comp
  
  Volume: 13 Issue: 6 Pages: 2489-2500
- DOI
  10.1021/acs.jctc.7b00188
- Peer Reviewed
- Data Source
  KAKENHI-PLANNED-26119006
[Journal Article] Tunnel Formation Inferred from the I-Form Structures of the Proton-Driven Protein Secretion Motor SecDF2017
- Author(s)
  Arata Furukawa, Kunihito Yoshikaie, Takaharu Mori, Hiroyuki Mori, Yusuke V. Morimoto, Yasunori Sugano, Shigehiro Iwaki, Tohru Minamino, Yuji Sugita, Yoshiki Tanaka, Tomoya Tsukazaki
- Journal Title
  
  Cell Reports
  
  Volume: 19 Issue: 5 Pages: 1-7
- DOI
  10.1016/j.celrep.2017.04.030
- Peer Reviewed / Acknowledgement Compliant / Open Access
- Data Source
  KAKENHI-PUBLICLY-15H01335, KAKENHI-PROJECT-15H05593, KAKENHI-PROJECT-15K14498, KAKENHI-PROJECT-17K07334, KAKENHI-PUBLICLY-17H05666, KAKENHI-PUBLICLY-17H05669, KAKENHI-PUBLICLY-17H05879, KAKENHI-PLANNED-26119006, KAKENHI-PLANNED-26119007, KAKENHI-PROJECT-15J08235, KAKENHI-PROJECT-15K06972, KAKENHI-PROJECT-16K14713, KAKENHI-PROJECT-25000013
[Journal Article] Slow-Down in Diffusion in Crowded Protein Solutions Correlates with Transient Cluster Formation2017
- Author(s)
  Grzegorz Nawrocki, Po-hung Wang, Isseki Yu, Yuji Sugita, and Michael Feig
- Journal Title
  
  J. Phys. Chem. B.
  
  Volume: 121 Issue: 49 Pages: 11072-11084
- DOI
  10.1021/acs.jpcb.7b08785
- Peer Reviewed / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-26119006
[Journal Article] Enhanced Conformational Sampling of N-Glycans in Solution with Replica State Exchange Metadynamics2017
- Author(s)
  Raimondas Galvelis, Suyong Re, and Yuji Sugita
- Journal Title
  
  Journal of Chemical Theory and Computation
  
  Volume: 13 Issue: 5 Pages: 1934-1942
- DOI
  10.1021/acs.jctc.7b00079
- Peer Reviewed / Acknowledgement Compliant
- Data Source
  KAKENHI-PROJECT-16K00415, KAKENHI-PLANNED-26119006
[Journal Article] Dynamics of Nitric Oxide Controlled by Protein Complex in Bacterial System2017
- Author(s)
  E. Terasakaa, K. Yamada, P.-H. Wang, K. Hosokawa, R. Yamagiwa, K. Matsumoto, S. Ishii, T. Mori, K. Yagi, H. Sawai, H. Arai, H. Sugimotoa, Y. Sugitac, Y. Shiroa, T. Tosha
- Journal Title
  
  Proc. Natl. Acd. SCI. USA
  
  Volume: 印刷中
- Peer Reviewed / Acknowledgement Compliant
- Data Source
  KAKENHI-PROJECT-26220807
[Journal Article] Dynamics of Nitric Oxide Controlled by Protein Complex in Bacterial System2017
- Author(s)
  Erina Terasaka, Kenta Yamada, Po-Hung Wang, Kanta Hosokawa, Raika Yamagiwa, Kimi Matsumoto, Shoko Ishii, Takaharu Mori, Kiyoshi Yagi, Hitomi Sawai, Hiroyuki Arai, Hiroshi Sugimoto, Yuji Sugita, Yoshitsugu Shiro and Takehiko Tosha
- Journal Title
  
  PNAS
  
  Volume: 114 Issue: 37 Pages: 9888-9893
- DOI
  10.1073/pnas.1621301114
- Peer Reviewed
- Data Source
  KAKENHI-PLANNED-26119006, KAKENHI-PROJECT-26220807, KAKENHI-PROJECT-17H03092, KAKENHI-PROJECT-15K07351
[Journal Article] GENESIS 1.1: A hybrid-parallel molecular dynamics simulator with enhanced sampling algorithms on multiple computational platforms2017
- Author(s)
  Kobayashi Chigusa、Jung Jaewoon、Matsunaga Yasuhiro、Mori Takaharu、Ando Tadashi、Tamura Koichi、Kamiya Motoshi、Sugita Yuji
- Journal Title
  
  Journal of Computational Chemistry
  
  Volume: 38 Issue: 25 Pages: 2193-2206
- DOI
  10.1002/jcc.24874
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-16K05526, KAKENHI-PLANNED-26119006
[Journal Article] Dimensionality of Collective Variables for Describing Conformational Changes of a Multi-Domain Protein2016
- Author(s)
  Y. Matsunaga, Yasuaki Komuro, Chigusa Kobayashi, Jaewoon Jung, Takaharu Mori, and Y. Sugita
- Journal Title
  
  The Journal of Physical Chemistry Letters
  
  Volume: 7 Issue: 8 Pages: 1446-1451
- DOI
  10.1021/acs.jpclett.6b00317
- Peer Reviewed / Acknowledgement Compliant
- Data Source
  KAKENHI-PUBLICLY-26120533, KAKENHI-PLANNED-26119006
[Journal Article] Anharmonic Vibrational Analyses of Pentapeptide Conformations Explored with Enhanced Sampling Simulations2016
- Author(s)
  H. Otaki, K. Yagi, S. Ishiuchi, M. Fujii, and Y. Sugita
- Journal Title
  
  Journal of Physical Chemistry B
  
  Volume: 120 Issue: 39 Pages: 10199-10213
- DOI
  10.1021/acs.jpcb.6b06672
- Peer Reviewed / Acknowledgement Compliant
- Data Source
  KAKENHI-PUBLICLY-16H00857, KAKENHI-PLANNED-25104008, KAKENHI-PLANNED-26119006
[Journal Article] 3.Mechanisms for Two-Step Proton Transfer Reactions in the Outward-Facing Form of MATE Transporter2016
- Author(s)
  Wataru Nishima, Wataru Mizukami, Yoshiki Tanaka, Ryuichiro Ishitani, Osamu Nureki, Yuji Sugita
- Journal Title
  
  Biophys. J
  
  Volume: 110 Issue: 6 Pages: 1346-1354
- DOI
  10.1016/j.bpj.2016.01.027
- Peer Reviewed / Acknowledgement Compliant / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-26119006, KAKENHI-PROJECT-25291011
[Journal Article] Dynamics and Interactions of OmpF and LPS: Influence on Pore Accessibility and Ion Permeability.2016
- Author(s)
  Dhilon S. Patel, Suyong Re, Emilia L. Wu, Yifei Qi, Phillip E. Klebba, Goran Widmalm, Min Sun Yeom, Yuji Sugita and Wonpil Im
- Journal Title
  
  Biophysical Journal
  
  Volume: 110 Issue: 4 Pages: 930-938
- DOI
  10.1016/j.bpj.2016.01.002
- Peer Reviewed / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-25330358
[Journal Article] Biomolecular interactions modulate macromolecular structure and dynamics in atomistic model of a bacterial cytoplasm2016
- Author(s)
  Yu I, Mori T, Ando T, Harada R, Jung J, Sugita Y, Feig M
- Journal Title
  
  eLife
  
  Volume: 5
- DOI
  10.7554/elife.19274
- Peer Reviewed / Acknowledgement Compliant / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-26119006, KAKENHI-PROJECT-15J03797, KAKENHI-PROJECT-25410025, KAKENHI-PROJECT-16H06164
[Journal Article] Molecular dynamics simulations of biological membranes and membrane proteins using enhanced conformational sampling algorithms2016
- Author(s)
  Takaharu Mori, Naoyuki Miyashita, Wonpil Im, Michael Feig, Yuji Sugita
- Journal Title
  
  Biochimica et Biophysica Acta (BBA) - Biomembranes
  
  Volume: in Press Issue: 7 Pages: 1635-1651
- DOI
  10.1016/j.bbamem.2015.12.032
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-26330341, KAKENHI-PROJECT-15H05594, KAKENHI-PLANNED-26119006
[Journal Article] Graphics Processing Unit Acceleration and Parallelization of GENESIS for Large-Scale Molecular Dynamics Simulations2016
- Author(s)
  Jung J, Naruse A, Kobayashi C, Sugita Y,
- Journal Title
  
  J. Chem. Theory Comput.
  
  Volume: 12 Issue: 10 Pages: 4947-4958
- DOI
  10.1021/acs.jctc.6b00241
- Peer Reviewed / Acknowledgement Compliant
- Data Source
  KAKENHI-PLANNED-26119006
[Journal Article] Hierachical domain-motion analysis of conformational changes in sarcoplasmic reticulum Ca2+-ATPase2015
- Author(s)
  Chigusa Kobayashi, Ryotaro Koike, Motonori Ota, and Yuji Sugita
- Journal Title
  
  PROTEINS: Structure, Function, and Bioinformatics
  
  Volume: 83 Issue: 4 Pages: 746-756
- DOI
  10.1002/prot.24763
- Peer Reviewed / Acknowledgement Compliant
- Data Source
  KAKENHI-PLANNED-26119006
[Journal Article] 5.Domain Motion Enhanced (DoME) Model for Efficient Conformational Sampling of Multidomain Proteins2015
- Author(s)
  Chigusa Kobayashi, Yasuhiro Matsunaga, Ryotaro Koike, Motonori Ota, Yuji Sugita
- Journal Title
  
  J. Phys. Chem. B
  
  Volume: 119 Issue: 46 Pages: 14584-14593
- DOI
  10.1021/acs.jpcb.5b07668
- Peer Reviewed / Acknowledgement Compliant
- Data Source
  KAKENHI-PLANNED-26119006, KAKENHI-PUBLICLY-26120533
[Journal Article] 11.GENESIS: A hybrid-parallel and multi-scale molecular dynamics simulator with enhanced sampling algorithms for biomolecular and cellular simulations2015
- Author(s)
  Jaewoon Jung, Takaharu Mori, Chigusa Kobayashi, Yasuhiro Matsunaga, Takao Yoda, Michael Feig, Yuji Sugita
- Journal Title
  
  WIREs Comp. Mol. Sci.
  
  Volume: 5 Issue: 4 Pages: 310-323
- DOI
  10.1002/wcms.1220
- Peer Reviewed / Acknowledgement Compliant / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-26119006, KAKENHI-PUBLICLY-26120533
[Journal Article] 7.Crystal Structures of SecYEG in Lipidic Cubic Phase Elucidate a Precise Resting and a Peptide-Bound State2015
- Author(s)
  Yoshiki Tanaka, Yasunori Sugano, Mizuki Takemoto, Takaharu Mori, Arata Furukawa, Tsukasa Kusakizako, Kaoru Kumazaki, Ayako Kashima, Ryuichiro Ishitani, Yuji Sugita, Osamu Nureki, Tomoya Tsukazaki
- Journal Title
  
  Cell report
  
  Volume: 13 Issue: 8 Pages: 1561-1568
- DOI
  10.1016/j.celrep.2015.10.025
- Peer Reviewed / Acknowledgement Compliant / Open Access
- Data Source
  KAKENHI-PLANNED-26119006, KAKENHI-PLANNED-26119007, KAKENHI-PROJECT-15J08129, KAKENHI-PROJECT-15J08235, KAKENHI-PROJECT-13J08353, KAKENHI-PROJECT-14J09020, KAKENHI-PROJECT-26291023
[Journal Article] REIN: Replica-Exchange INterface for Simulating Protein Dynamics and Function2015
- Author(s)
  Naoyuki Miyashita, Suyong Re, Yuji Sugita
- Journal Title
  
  International Journal of Quantum Chemistry
  
  Volume: 115 Issue: 5 Pages: 325-332
- DOI
  10.1002/qua.24785
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-25330358, KAKENHI-PROJECT-26330341
[Journal Article] 9.Sequential data assimilation for single-molecule FRET photon-counting data2015
- Author(s)
  Yasuhiro Matsunaga, Akinori Kidera, Yuji Sugita
- Journal Title
  
  J. Chem. Phys.
  
  Volume: 142 Issue: 21 Pages: 214115-214115
- DOI
  10.1063/1.4921983
- Peer Reviewed / Acknowledgement Compliant
- Data Source
  KAKENHI-PLANNED-26119006, KAKENHI-PUBLICLY-26120533
[Journal Article] Rational design of crystal contact-free space in protein crystals for analyzing spatial distribution of motions within protein molecules.2015
- Author(s)
  Matsuoka R, Shimada A, Komuro Y, Sugita Y, Kohda D
- Journal Title
  
  Protein Science
  
  Volume: 25 Issue: 3 Pages: 754-768
- DOI
  10.1002/pro.2867
- Peer Reviewed / Acknowledgement Compliant
- Data Source
  KAKENHI-PLANNED-26119002, KAKENHI-PLANNED-26119006
[Journal Article] Mosaic of water orientation structures at a neutral zwitterion lipid/water interface revealed by molecular dynamics simulations2014
- Author(s)
  Syong RE, Wataru NISHIMA, Tahei TAHARA and Yuji SUGITA
- Journal Title
  
  J. Phys. Chem. Lett.
  
  Volume: 5 Issue: 24 Pages: 4343-4348
- DOI
  10.1021/jz502299m
- Peer Reviewed / Acknowledgement Compliant
- Data Source
  KAKENHI-PLANNED-25104005, KAKENHI-PROJECT-25330358, KAKENHI-PLANNED-26119006
[Journal Article] CHARMM Force-fields with Modified Polyphosphate Parameters Allow Stable Simulation of the ATP-Bound Structure of Ca2+-ATPase2014
- Author(s)
  Yasuaki Komuro, Suyong Re, Chigusa Kobayashi, Eiro Muneyuki and Yuji Sugita
- Journal Title
  
  Journal of Chemical Theory and Computation
  
  Volume: 10 Issue: 9 Pages: 4133-4142
- DOI
  10.1021/ct5004143
- Peer Reviewed / Acknowledgement Compliant
- Data Source
  KAKENHI-PROJECT-14J05682, KAKENHI-PROJECT-24570187, KAKENHI-PROJECT-25330358, KAKENHI-PUBLICLY-26103528
[Journal Article] Crystal structure of α5β1 integrin ectodomain : Atomic details of the fibronectin receptor2012
- Author(s)
  Nagae, M., Re, S., Mihara, E., Nogi, T., Sugita, Y., Takagi, J.
- Journal Title
  
  Journal of Cell Biology
  
  Volume: (In press)
- Peer Reviewed
- Data Source
  KAKENHI-PUBLICLY-22121521
[Journal Article] Structural Diversity and Changes in Conformational □Equilibria of Biantennary Complex-Type N-Glycans in Water Revealed by Replica-Exchange Molecular Dynamics Simulation2011
- Author(s)
  Re, S., Miyashita, N., Yamaguchi, Y., Sugita, Y.
- Journal Title
  
  Biophysical Journal (Letter)
  
  Volume: 101 Issue: 10 Pages: L44-L46
- DOI
  10.1016/j.bpj.2011.10.019
- Peer Reviewed
- Data Source
  KAKENHI-PUBLICLY-22121521
[Journal Article] Insight into the relationship between Ca^<2+>-affinity and shielding of bulk water in the Ca^<2+>-pump from molecular dynamics simulations.2010
- Author(s)
  Y.Sugita, et al.
- Journal Title
  
  Proc.Natl.Acad.Sci.USA
  
  Volume: 107 Pages: 21465-21469
- Peer Reviewed
- Data Source
  KAKENHI-PUBLICLY-22121521
[Journal Article] 京速コンピュータで実現する次世代の生命科学シミュレーション2010
- Author(s)
  杉田有治
- Journal Title
  
  日本の科学者
  
  Volume: 45 Pages: 674-679
- Peer Reviewed
- Data Source
  KAKENHI-PUBLICLY-22121521
[Journal Article] Transmembrane Structures of Amyloid Precursor Protein Dimer Predicted by Replica-Exchange Molecular Dynamics Simulations2009
- Author(s)
  N. Miyashita, J. E. Straub, D. Thirumalai, Y. Sugita
- Journal Title
  
  J. Am. Chem. Soc. 131(10)
  
  Pages: 3438-3439
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-15083201
[Journal Article] Free-energy landscapes of proteins in solution by generalized-ensemble simulations2009
- Author(s)
  Y. Sugita
- Journal Title
  
  Frontiers in Bioscience 14
  
  Pages: 1292-1303
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-15083201
[Journal Article] Mg^<2+>-sensing mechanism of Mg^<2+> transporter MgtE probed by molecular dynamics study2008
- Author(s)
  R. Ishitani, Y. Sugita, N. Dohmae, N. Furuya, M. Hattori, O. Nureki
- Journal Title
  
  Proc. Natl. Acad. Sci. USA. 105(40)
  
  Pages: 15393-15398
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-15083201
[Journal Article] Generalized-Ensemble Algorithms for Protein Folding Simulations2008
- Author(s)
  Y. Sugita, A. Mitsutake, Y. Okamoto
- Journal Title
  
  Lecture Notes in Physics 736
  
  Pages: 369-407
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-15083201
[Journal Article] カルシウムポンプの機能制御機構2008
- Author(s)
  杉田有治
- Journal Title
  
  生化学 61-6
  
  Pages: 582-584
- NAID
  10022594597
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-15083201
[Journal Article] ぞくぞくとわかってきた膜を隔てたイオン輸送装置構造2008
- Author(s)
  杉田有治
- Journal Title
  
  生物物理 48(6)
  
  Pages: 330-332
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-15083201
[Journal Article] Conformational transition of Sec machinery inferred from bacterial SecYE structures2008
- Author(s)
  T. Tsukazaki, H. Mori, S. Fukai, R. Ishitani, T. Mori, N. Dohmae, A. Perederina, Y. Sugita, D.G. Vassylyev, K. Ito, O. Nureki
- Journal Title
  
  Nature 455
  
  Pages: 938-992
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-15083201
[Journal Article] カルシウムポンプの機能制御機構2008
- Author(s)
  杉田有治
- Journal Title
  
  生化学 80
  
  Pages: 917-924
- NAID
  10022594597
- Data Source
  KAKENHI-PROJECT-15083201
[Journal Article] 生体分子の構造探索の理論2008
- Author(s)
  杉田有治
- Journal Title
  
  化学と工業 61-6
  
  Pages: 582-584
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-15083201
[Journal Article] Replica-exchange molecular dynamics simulations of diffracted X-ray tracking2007
- Author(s)
  Y. Kawashima, Y.C. Sasaki, Y. Sugita, T. Yoda, Y. Okamoto
- Journal Title
  
  Molecular simulation 33
  
  Pages: 97-102
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-15083201
[Journal Article] Cooperative Folding Mechanism of a b-Hairpin Peptide Studied by Using a Multicanonical Replica-Exchange Molecular Dynamics Simulation2007
- Author(s)
  Yoda T, Sugita Y, Okamoto Y
- Journal Title
  
  PROTEINS : Structure, Function, and Bioinformatics 66
  
  Pages: 846-859
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-15083201
[Journal Article] New implementation of a combined quantum mechanical and molecular mechanical method using modified generalized hybrid orbitals2007
- Author(s)
  J. Jung, C.H. Choi, Y. Sugita, S. Ten-no
- Journal Title
  
  J. Chem. Phys. 127
  
  Pages: 204102-204102
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-15083201
[Journal Article] Physical basis for characterizing native structures of proteins2007
- Author(s)
  Y. Harano, R. Roth, Y. Sugita, M. Ikeguchi, M. Kinoshita
- Journal Title
  
  Chem. Phys. Lett. 437
  
  Pages: 112-116
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-15083201
[Journal Article] Structural Changes in the Cytoplasmic Domain of Phospholamban at Serl6 : A Molecular Dynamics Study2006
- Author(s)
  Sugita et al.
- Journal Title
  
  Biochemistry 45
  
  Pages: 11752-11761
- Data Source
  KAKENHI-PROJECT-15083201
[Journal Article] 膜蛋白質の分子動力学2006
- Author(s)
  杉田有治 et al.
- Journal Title
  
  物性研究 50
  
  Pages: 1271-1277
- Data Source
  KAKENHI-PROJECT-15083201
[Journal Article] Structural changes of the cytoplasmic domain of phospholamban by phosphorylation at Ser16: A molecular dynamics study.2006
- Author(s)
  Y. Sugita
- Journal Title
  
  Biochemistry 45
  
  Pages: 11752-11761
- Data Source
  KAKENHI-PROJECT-14GS0308
[Journal Article] 膜蛋白質の分子動力学2006
- Author(s)
  杉田有治, 池口満徳
- Journal Title
  
  物性研究 50
  
  Pages: 1271-1277
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-15083201
[Journal Article] Structural Changes in the Cytoplasmic Domain of Phospholamban by Phosphorylation at Ser16 : A Molecular Dynamics Study2006
- Author(s)
  Sugita Y, Miyashita N, Yoda T, Ikeguchi M, Toyoshima C
- Journal Title
  
  Biochemistry 45
  
  Pages: 11752-11761
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-15083201
[Journal Article] Structures of a peptide fragment of β_2-microgloblin studied by replica-exchange molecular dynamics simulations : towards the understanding of the mechanism of amyloid formation2005
- Author(s)
  Nishino M, Sugita Y, Yoda T, Okamoto Y
- Journal Title
  
  FEBS Lett. 579
  
  Pages: 5425-5429
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-15083201
[Journal Article] Structural role of countertransport revealed in Ca^<2+> pump crystal structure in the absence of Ca^<2+>2005
- Author(s)
  Obara K, Miyashita N, Xu C, Toyoshima I, Sugita Y, Ineshi G, Toyoshima C
- Journal Title
  
  Proc. Natl. Acid, Sci. USA. 102
  
  Pages: 14489-14496
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-15083201
[Journal Article] Molecular mechanism for stabilizing a short helical peptide studied by generalized-ensemble simulations with explicit solvent.2005
- Author(s)
  Sugita et al.
- Journal Title
  
  Biophys.J. 88
  
  Pages: 3180-3190
- Data Source
  KAKENHI-PROJECT-15083201
[Journal Article] Molecular mechanism for stabilizing a short helical peptide studied by generalized-ensemble simulations with explicit solvent2005
- Author(s)
  Sugita Y, Okamoto Y
- Journal Title
  
  Biophysical J. 88
  
  Pages: 3180-3190
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-15083201
[Journal Article] Molecular dynamics simulations of DNA dimers based on replica-exchange umbrella sampling. II. Free energy analysis2005
- Author(s)
  Murata K, Sugita Y, Okamoto Y
- Journal Title
  
  J. Theor. Comp. Chem. 4
  
  Pages: 433-448
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-15083201
[Journal Article] Protonation of the acidic residues in the transmembrane cation-binding sites of the Ca^<2+>-pump2005
- Author(s)
  Sugita Y, Miyashita N, Ikeguchi M, Kidera A, Toyoshima C
- Journal Title
  
  J. Am. Chem. Soc. 127
  
  Pages: 6150-6151
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-15083201
[Journal Article] カルシウムポンプの構造と機能2005
- Author(s)
  杉田有治, 豊島近
- Journal Title
  
  蛋白質・核酸・酵素, 増刊号「生命秩序を担う生体超分子」 50
  
  Pages: 1271-1277
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-15083201
[Journal Article] Protonation of the acidic residues in the transmembrane cation-binding sites of the Ca^<2+>-pump2005
- Author(s)
  Sugita et al.
- Journal Title
  
  J.Am.Chem.Soc. 127
  
  Pages: 6150-6151
- Data Source
  KAKENHI-PROJECT-15083201
[Journal Article] Protonation of the acidic residues in the transmembrane cation-binding sites of the Ca^<2+> pump.2005
- Author(s)
  Y.Sugita
- Journal Title
  
  J. Am. Chem. Soc. 127
  
  Pages: 6150-6451
- Data Source
  KAKENHI-PROJECT-14GS0308
[Journal Article] Molecular dynamics simulations of DNA dimers based on replica-exchange umbrella sampling. I. Test of sampling efficiency2005
- Author(s)
  Murata K, Sugita Y, Okamoto Y
- Journal Title
  
  J. Theor. Comp. Chem. 4
  
  Pages: 411-432
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-15083201
[Journal Article] Effects of the Fixed End in Single-Molecular Imaging Techiques : A Replica Exchange Molecular Dynamics Simulation2005
- Author(s)
  Kawashima Y, Sugita Y, Yoda T, Okamoto Y
- Journal Title
  
  Chem. Phys. Lett. 414
  
  Pages: 449-455
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-15083201
[Journal Article] Free energy calculations for DNA base stacking by replica-exchange umbrella sampling2004
- Author(s)
  K. Murata, Y. Sugita, Y. Okamoto
- Journal Title
  
  Chem. Phys. Lett. 385
  
  Pages: 1-7
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-15083201
[Journal Article] Secondary-Structure Preferences of Force Fields for Proteins Evaluated by Generalized-Ensemble Simulations2004
- Author(s)
  T. Yoda, Y. Sugita, Y. Okamoto
- Journal Title
  
  Chem. Phys.
  
  Pages: 269-283
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-15083201
[Journal Article] Comparisons of Force Fields for Proteins by Generalized-Ensemble Simulations2004
- Author(s)
  T. Yoda, Y. Sugita, Y. Okamoto
- Journal Title
  
  Chem. Phys. Lett. 386
  
  Pages: 460-467
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-15083201
[Presentation] Protein Functions in Crowded Cellular Environments2024
- Author(s)
  Yuji Sugita
- Organizer
  The 6th Symposium on Biophysics Postgraduate Research in Hong Kong
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-19H05645
[Presentation] NMR studies of multi-domain adaptor proteins in signal transduction pathways2024
- Author(s)
  Yutaka Ito，Teppei Ikeya，Sayeesh P.M.，Mao Oide，Yuji Sugita
- Organizer
  TJ2024 (Taiwan-Japan NMR Symposium 2024)
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-19H05645
[Presentation] Refinement of Markov State Model using experimental data and nonlinear dimensional reduction methods2024
- Author(s)
  Yuji Sugita
- Organizer
  ACS Symposium on Markov State Modeling of Conformational Dynamics in the Wake of Machine Learning
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-21H05249
[Presentation] Integrated Modeling of Flexible Multi-Domain Protein Structures in Solution2024
- Author(s)
  Yuji Sugita, Mao Oide, Teppei Ikeya, Yutaka Ito
- Organizer
  9th Polish-Korean Conference on Protein Folding
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-19H05645
[Presentation] Protein Functions in Crowded Cellular Environments2024
- Author(s)
  Yuji Sugita
- Organizer
  The 6th Symposium on Biophysics Postgraduate Research in Hong Kong
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-21H05249
[Presentation] Refinement of Markov State Model using experimental data and nonlinear dimensional reduction methods2024
- Author(s)
  Yuji Sugita
- Organizer
  ACS Symposium on Markov State Modeling of Conformational Dynamics in the Wake of Machine Learning
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-19H05645
[Presentation] Integrated Modeling of Flexible Multi-Domain Protein Structures in Solution2024
- Author(s)
  Yuji Sugita, Mao Oide, Teppei Ikeya, Yutaka Ito
- Organizer
  9th Polish-Korean Conference on Protein Folding
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-21H05249
[Presentation] 細胞内環境における蛋白質の構造・ダイナミクス・機能2023
- Author(s)
  杉田有治
- Organizer
  第22回日本蛋白質科学会年会
- Invited
- Data Source
  KAKENHI-PLANNED-21H05249
[Presentation] Multi-scale molecular dynamics simulations on protein function in intracellular environments2023
- Author(s)
  Yuji Sugita
- Organizer
  CCP2023
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-21H05249
[Presentation] Computational studies of conformational dynamics of membrane transporters and pumps2023
- Author(s)
  Yuji Sugita
- Organizer
  10th Asian Biological Inorganic Chemistry Conference
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-21H05249
[Presentation] Monomeric Structures of GRB2 in Solution by Integrated Modeling2023
- Author(s)
  Yuji Sugita, Mao Oide, Teppei Ikeya, Yutaka Ito
- Organizer
  EMBO workshop on Computational Structural Biology
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-21H05249
[Presentation] Enhanced Conformational Sampling for Protein Dynamics and Function2023
- Author(s)
  Yuji Sugita
- Organizer
  8th Polish-Korean Conference on Protein Folding
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-19H05645
[Presentation] Conformational Dynamics and Functions of Proteins in Crowded Cellular Environments2023
- Author(s)
  Yuji Sugita
- Organizer
  BPS Thematic Meeting Hamburg
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-21H05249
[Presentation] Molecular dynamics simulation of the substrate channeling in tryptophan synthetase2023
- Author(s)
  優乙石, 伊東真吾, 八木清, 杉田有治
- Organizer
  第61回生物物理学会年会
- Data Source
  KAKENHI-PROJECT-19H05645
[Presentation] Protein Dynamics and Functions using enhanced MD simulations2023
- Author(s)
  Yuji Sugita
- Organizer
  The 23rd Sanibel Meeting
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-19H05645
[Presentation] How cellular environments are regulated by non-specific molecular interaction2023
- Author(s)
  Yuji Sugita
- Organizer
  Biomolecules and Nanostructures 8
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-19H05645
[Presentation] Crowding effects on protein structure, dynamics, and functions2023
- Author(s)
  Yuji Sugita
- Organizer
  The 21st KIAS Conference on Protein Folding and Function
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-21H05249
[Presentation] Analysis of the mechanism underlying multivalent interactions between GRB2 and SOS1 and their LLPS using solution NMR2023
- Author(s)
  Teppei Ikeya，Mao Oide，W. Ren，Keita Tateno，Takami Ando，Haruka Sugasawa，Yuji Sugita，Yutaka Ito
- Organizer
  第61回生物物理学会年会
- Data Source
  KAKENHI-PROJECT-19H05645
[Presentation] Protein dynamics and functions using enhanced MD simulations2023
- Author(s)
  Yuji Sugita
- Organizer
  CECAM Workshop
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-19H05645
[Presentation] Regulation of Biomolecular Condensation Studied with Large-Scale Coarse-Grained Molecular Dynamics Simulations in GENESIS2023
- Author(s)
  Cheng Tan, Ai Niitsu, Jaewoon Jung, Yuji Sugita
- Organizer
  第61回日本生物物理学会年会
- Invited
- Data Source
  KAKENHI-PLANNED-21H05249
[Presentation] Regulation of Biomolecular Condensation Studied with Large-Scale Coarse-Grained Molecular Dynamics Simulations in GENESIS2023
- Author(s)
  Cheng Tan, Ai Niitsu, Jaewoon Jung, Yuji Sugita
- Organizer
  第61回生物物理学会年会
- Invited
- Data Source
  KAKENHI-PROJECT-19H05645
[Presentation] Extension of the Implicit Solvent Lipid Force Field, iSoLF, for the simulation of large multi-component lipidic systems using GENESIS2023
- Author(s)
  Diego Ugarte, Shoji Takada, Yuji Sugita
- Organizer
  第60回日本生物物理学会年会
- Data Source
  KAKENHI-PLANNED-21H05249
[Presentation] GRB2とSOS1による多価相互作用と液液相分離の溶液NMR解析2023
- Author(s)
  池谷鉄兵，菅澤はるか，富樫直之，林俊文，美川務，杉田有治，伊藤隆
- Organizer
  第62回NMR討論会
- Data Source
  KAKENHI-PROJECT-19H05645
[Presentation] 分子動力学ソフトウェアGENESISの開発と細胞内における蛋白質動態解析2023
- Author(s)
  杉田有治
- Organizer
  兵庫県MI研究会
- Invited
- Data Source
  KAKENHI-PLANNED-21H05249
[Presentation] 計算科学で挑む細胞内環境の生物学2023
- Author(s)
  杉田有治
- Organizer
  第48回生体分子科学討論会
- Invited
- Data Source
  KAKENHI-PLANNED-21H05249
[Presentation] Monomeric Structures of GRB2 in Solution by Integrated Modeling2023
- Author(s)
  Yuji Sugita, Mao Oide, Teppei Ikeya, Yutaka Ito
- Organizer
  EMBO workshop on Computational Structural Biology
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-19H05645
[Presentation] Multi-scale molecular dynamics simulations on protein function in intracellular environments2023
- Author(s)
  Yuji Sugita
- Organizer
  CCP2023
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-19H05645
[Presentation] Accurate Langevin integration for isothermal-isobaric condition with a large time step2023
- Author(s)
  Jaewoon Jung, Yuji Sugita
- Organizer
  CCP2023
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-21H05249
[Presentation] Crowding effects on protein structure, dynamics, and functions2023
- Author(s)
  Yuji Sugita
- Organizer
  The 21st KIAS Conference on Protein Folding and Function
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-19H05645
[Presentation] Protein Dynamics and Functions using enhanced MD simulations2023
- Author(s)
  Yuji Sugita
- Organizer
  The 23rd Sanibel Meeting
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-21H05249
[Presentation] Binding free energy landscape of c-Src kinase to its inhibitors sampled by molecular dynamics simulations: effect of ligand size and flexibility2023
- Author(s)
  Ai Shinobu, Suyong Re, Yuji Sugita
- Organizer
  BPS2023
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-19H05645
[Presentation] Coarse-grained modeling and simulations of protein and lipid dynamics2023
- Author(s)
  Yuji Sugita
- Organizer
  MBSJ
- Invited
- Data Source
  KAKENHI-PROJECT-19H05645
[Presentation] Coarse-grained modeling and simulations of protein and lipid dynamics2023
- Author(s)
  Yuji Sugita
- Organizer
  MBSJ
- Invited
- Data Source
  KAKENHI-PLANNED-21H05249
[Presentation] Enhanced Conformational Sampling for Protein Dynamics and Function2023
- Author(s)
  Yuji Sugita
- Organizer
  8th Polish-Korean Conference on Protein Folding
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-21H05249
[Presentation] Protein dynamics and functions using enhanced MD simulations2023
- Author(s)
  Yuji Sugita
- Organizer
  CECAM Workshop
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-21H05249
[Presentation] Accurate Langevin integration for isothermal-isobaric condition with a large time step2023
- Author(s)
  Jaewoon Jung, Yuji Sugita
- Organizer
  CCP2023
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-19H05645
[Presentation] Molecular dynamics simulation of large multi-component lipid bilayers in GENESIS using the iSoLF coarse-grained model2023
- Author(s)
  Diego Ugarte, Shoji Takada, Yuji Sugita
- Organizer
  The 5th R-CCS International Symposium
- Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-21H05249
[Presentation] How cellular environments are regulated by non-specific molecular interaction2023
- Author(s)
  Yuji Sugita
- Organizer
  Biomolecules and Nanostructures 8
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-21H05249
[Presentation] 静電相互作用の計算コストを抑えた自由エネルギー摂動法の開発2022
- Author(s)
  尾嶋拓, 杉田有治
- Organizer
  第36回分子シミュレーション討論会
- Data Source
  KAKENHI-PROJECT-19H05645
[Presentation] Reduced efficacy of a Src kinase inhibitor in crowded protein solution2022
- Author(s)
  Yuji Sugita
- Organizer
  Prof. Sihyun Ham Memorial Symposium
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-21H05249
[Presentation] 分子動力学計算によるF1-ATPaseのリン酸放出経路の探索2022
- Author(s)
  本橋昌大, 大出真央, 宗行英朗, 杉田有治
- Organizer
  第22回日本蛋白質科学会年会
- Data Source
  KAKENHI-PROJECT-19H05645
[Presentation] Microscopic Investigation on the Protein Aggregation Inhibition by ATP in Cell2022
- Author(s)
  優乙石, 杉田有治
- Organizer
  第9回HPCIシステム利用研究課題成果報告会
- Data Source
  KAKENHI-PROJECT-19H05645
[Presentation] 常磁性NMRを用いたマルチドメイン蛋白質GRB2の立体構造解析2022
- Author(s)
  安藤考史，菅澤はるか，館野桂太，田端真彩子，美川務，宮野入洋平，川端庸平，Hisham Dokainish，Weitong Ren，大出真央，寺内勉，猪股晃介，三島正規，甲斐荘正恒，杉田有治，池谷鉄兵，伊藤隆
- Organizer
  第61回NMR討論会
- Data Source
  KAKENHI-PROJECT-19H05645
[Presentation] 計算科学で挑む細胞内環境の生物学2022
- Author(s)
  杉田有治
- Organizer
  第48回生体分子科学討論会
- Invited
- Data Source
  KAKENHI-PROJECT-19H05645
[Presentation] Development of the free-energy perturbation method toward drug discovery on supercomputer Fugaku2022
- Author(s)
  尾嶋拓, 杉田有治
- Organizer
  第60回日本生物物理学会年会
- Invited
- Data Source
  KAKENHI-PROJECT-19H05645
[Presentation] Multi-scale simulations of large biological systems on Fugaku2022
- Author(s)
  Yuji Sugita
- Organizer
  R-CCS symposium
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-21H05249
[Presentation] 新型コロナウイルススパイクタンパク質の糖鎖による構造安定性2022
- Author(s)
  杉田有治
- Organizer
  第19回糖鎖科学コンソーシアムシンポジウム
- Invited
- Data Source
  KAKENHI-PROJECT-19H05645
[Presentation] Stability and dynamics of de novo designed transmembrane peptide barrels2022
- Author(s)
  Ai Niitsu, Jaewoon Jung, and Yuji Sugita
- Organizer
  第60回日本生物物理学会年会
- Invited
- Data Source
  KAKENHI-PROJECT-19H05645
[Presentation] Multi-scale simulations of large biological systems on Fugaku2022
- Author(s)
  Yuji Sugita
- Organizer
  R-CCS symposium
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-19H05645
[Presentation] Free Energy Perturbation Method in GENESIS2022
- Author(s)
  尾嶋拓, 杉田有治
- Organizer
  CBI学会2022年大会
- Data Source
  KAKENHI-PROJECT-19H05645
[Presentation] 分子動力学ソフトウェアGENESISの開発と細胞内における蛋白質動態解析2022
- Author(s)
  杉田有治
- Organizer
  兵庫県MI研究会
- Invited
- Data Source
  KAKENHI-PROJECT-19H05645
[Presentation] Conformational Dynamics and Functions of Proteins in Crowded Cellular Environments2022
- Author(s)
  Yuji Sugita
- Organizer
  BPS Thematic Meeting Hamburg
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-19H05645
[Presentation] De novo design of membrane coiled-coil barrels2022
- Author(s)
  Ai Niitsu, Andrew R Thomson, Alistair Scott, Jason T Sengel, Kozhinjampara R Mahendran, Yuji Sugita, R Leo Brady, Mark I Wallace, Hagan Bayley, and Derek N Woolfson
- Organizer
  Alpbach Workshop: Coiled coils, fibrous & repeat proteins
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-19H05645
[Presentation] 静電相互作用計算を高速化した自由エネルギー摂動法の開発2022
- Author(s)
  尾嶋拓, 杉田有治
- Organizer
  第22回日本蛋白質科学会年会
- Data Source
  KAKENHI-PROJECT-19H05645
[Presentation] Reduced efficacy of a Src kinase inhibitor in crowded protein solution2022
- Author(s)
  Yuji Sugita
- Organizer
  Prof. Sihyun Ham Memorial Symposium
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-19H05645
[Presentation] Residue-level coarse-grained models in GENESIS for large-scale molecular dynamics simulations2022
- Author(s)
  Yuji Sugita
- Organizer
  ACS Spring 2022
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-21H05249
[Presentation] Stability and interaction of macromolecules altered by nucleoside triphosphates in cellular crowding2022
- Author(s)
  優乙石, 山崎竜人, Feig Michael, 杉田有治
- Organizer
  第60回生物物理学会年会
- Data Source
  KAKENHI-PROJECT-19H05645
[Presentation] マルチドメイン蛋白質GRB2とSOS1-PRM領域の相互作用解析2022
- Author(s)
  館野桂太，菅澤はるか，安藤考史，田端真彩子，美川務，猪股晃介，甲斐荘正恒，三島正規，杉田有治，池谷鉄兵，伊藤隆
- Organizer
  第61回NMR討論会
- Data Source
  KAKENHI-PROJECT-19H05645
[Presentation] Free-energy calculations of protein-ligand binding in solution and crowded environments2022
- Author(s)
  Yuji Sugita
- Organizer
  WCB2022
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-19H05645
[Presentation] 細胞内環境の生物物理学2022
- Author(s)
  杉田有治
- Organizer
  東京大学理学部物理コロキウム
- Invited
- Data Source
  KAKENHI-PROJECT-19H05645
[Presentation] Binding free energy landscapes of Src Kinase to its inhibitors sampled by two-dimensional replica exchange molecular dynamics simulations2022
- Author(s)
  信夫愛、李秀栄、杉田有治
- Organizer
  第60回日本生物物理学会年会
- Invited
- Data Source
  KAKENHI-PROJECT-19H05645
[Presentation] Computational studies of conformational dynamics of membrane transporters and pumps2022
- Author(s)
  Yuji Sugita
- Organizer
  10th Asian Biological Inorganic Chemistry Conference
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-19H05645
[Presentation] 分子動力学計算によるトリプトファン合成酵素におけるアロステリック機構の解明2022
- Author(s)
  伊東真吾,八木清,杉田有治
- Organizer
  第22回日本蛋白質科学会年会
- Data Source
  KAKENHI-PROJECT-19H05645
[Presentation] Src Kinase inhibitor binding free energy landscape sampled by Molecular-dynamics simulations: effect of ligand size and flexibility2022
- Author(s)
  信夫愛、李秀栄、杉田有治
- Organizer
  第22回日本蛋白質科学会年会
- Data Source
  KAKENHI-PROJECT-19H05645
[Presentation] クライオ電子顕微鏡像に基づく蛋白質動態の自由エネルギー地形推定法の開発と検討2022
- Author(s)
  大出真央, 杉田有治
- Organizer
  第22回日本蛋白質科学会年会
- Data Source
  KAKENHI-PROJECT-19H05645
[Presentation] 細胞内環境における蛋白質の構造・ダイナミクス・機能2022
- Author(s)
  杉田有治
- Organizer
  第22回日本蛋白質科学会年会
- Invited
- Data Source
  KAKENHI-PROJECT-19H05645
[Presentation] Cryo-EM flexible fitting refinement with automatic error fixing for de novo protein structure modeling2021
- Author(s)
  森貴治、寺師玄記、松岳大輔、木原大亮、杉田有治
- Organizer
  第59回日本生物物理学会年会
- Data Source
  KAKENHI-PROJECT-19H05645
[Presentation] Parallel computing algorithms in molecular dynamics simulations for extremely large-scale biological systems2021
- Author(s)
  Yuji Sugita
- Organizer
  HITS Colloquium
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-21H05249
[Presentation] 新型コロナウイルス表面のタンパク質動的構造予測2021
- Author(s)
  杉田有治
- Organizer
  HPCIフォーラム
- Invited
- Data Source
  KAKENHI-PROJECT-19H05645
[Presentation] Finding the reaction path of metalloenzyme using QM/MM in GENESIS2021
- Author(s)
  Kiyoshi Yagi, Yuji Sugita
- Organizer
  Pachifichem symposium (#83)
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-19H05645
[Presentation] Molecular mechanisms for conformational changes and chemical reactions in the Ca2+-ATPase2021
- Author(s)
  Yuji Sugita
- Organizer
  Pachifichem symposium (#206)
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-19H05645
[Presentation] 富岳を用いた新型コロナウイルス表面のスパイクタンパク質動的構造予測2021
- Author(s)
  杉田有治
- Organizer
  近畿化学協会コンピュータ化学部会
- Invited
- Data Source
  KAKENHI-PROJECT-19H05645
[Presentation] Intrinsic Conformational Flexibility of SARS-CoV-2 Spike-Protein Simulated on Fugaku2021
- Author(s)
  Yuji Sugita
- Organizer
  The 3rd R-CCS International Symposium
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-19H05645
[Presentation] How macromolecular crowding environments affect protein-ligand binding kinetics and thermodynamics2021
- Author(s)
  Yuji Sugita
- Organizer
  Pachifichem symposium
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-21H05249
[Presentation] Capturing drastic state transitions of biological macromolecules by molecular dynamics simulation and nonlinear dimensionality reduction2021
- Author(s)
  大出真央, 杉田有治
- Organizer
  第59回日本生物物理学会年会
- Data Source
  KAKENHI-PROJECT-19H05645
[Presentation] In situ Analysis of Protein Dynamics with All atom Cytoplasm Simulations2021
- Author(s)
  優乙石, Po-hung Wang , 杉田有治
- Organizer
  第８回HPCIシステム利用研究課題成果報告会
- Data Source
  KAKENHI-PROJECT-19H05645
[Presentation] Procedures to obtain reliable free-energy profiles of conformational changes in membrane transporters2021
- Author(s)
  Yuji Sugita
- Organizer
  ACS Fall 2021
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-19H05645
[Presentation] Multi-scale MD simulations using GENESIS on Fugaku2021
- Author(s)
  Yuji Sugita
- Organizer
  The 1st Fugaku Bio-supercomputing Workshop on Cellular-Scale Molecular Dynamics Simulations
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-19H05645
[Presentation] Mechanisms for conformational changes of proteins upon ligand bindings2021
- Author(s)
  Yuji Sugita
- Organizer
  第59回日本生物物理学会年会
- Invited
- Data Source
  KAKENHI-PROJECT-19H05645
[Presentation] Molecular mechanisms for conformational changes and chemical reactions in the Ca2+-ATPase2021
- Author(s)
  Yuji Sugita
- Organizer
  Pachifichem symposium
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-21H05249
[Presentation] Enhanced Sampling Techniques2021
- Author(s)
  Yuji Sugita
- Organizer
  CECAM CHARMM-GUI Workshop
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-19H05645
[Presentation] Development of Trajectory Analyzer for Cellular-Scale Molecular Dynamics Simulations2021
- Author(s)
  優乙石, 杉田有治
- Organizer
  第59回日本生物物理学会
- Data Source
  KAKENHI-PROJECT-19H05645
[Presentation] Parallel computing algorithms in molecular dynamics simulations for extremely large-scale biological systems2021
- Author(s)
  Yuji Sugita
- Organizer
  HITS Colloquium
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-19H05645
[Presentation] Mechanisms for conformational changes of proteins upon ligand bindings2021
- Author(s)
  Yuji Sugita
- Organizer
  Polish-Korean Protein Folding Conference
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-19H05645
[Presentation] Mechanisms for conformational changes of proteins upon ligand bindings2021
- Author(s)
  杉田有治
- Organizer
  第59回日本生物物理学会年会
- Invited
- Data Source
  KAKENHI-PLANNED-21H05249
[Presentation] 分子動力学シミュレーションによる蛋白質の動的構造と基質結合：分子混雑環境の影響とSARS-CoV-2スパイク蛋白質に関する計算2021
- Author(s)
  杉田有治
- Organizer
  構造活性フォーラム2021
- Invited
- Data Source
  KAKENHI-PROJECT-19H05645
[Presentation] 分子動力学計算プログラムGENESISにおけるQM/MM法の開発と応用2021
- Author(s)
  八木清、杉田有治
- Organizer
  第23回理論化学討論会
- Data Source
  KAKENHI-PROJECT-19H05645
[Presentation] How macromolecular crowding environments affect protein-ligand binding kinetics and thermodynamics2021
- Author(s)
  Yuji Sugita
- Organizer
  Pachifichem symposium (#200)
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-19H05645
[Presentation] Conformational flexibility and stability of SARS-CoV-2 spike protein in solution2021
- Author(s)
  Yuji Sugita
- Organizer
  ACS Spring 2021
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-19H05645
[Presentation] Development of GENESIS MD software on Fugaku supercomputer for understanding large scale biomolecular phenomena in cellular environments2021
- Author(s)
  Jaewoon Jung, Chigusa Kobayashi, Yuji Sugita
- Organizer
  Pachifichem symposium
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-21H05249
[Presentation] Development of GENESIS MD software on Fugaku supercomputer for understanding large scale biomolecular phenomena in cellular environments2021
- Author(s)
  Jaewoon Jung, Chigusa Kobayashi, Yuji Sugita
- Organizer
  Pachifichem symposium
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-19H05645
[Presentation] Optimized hydrogen mass repartitioning scheme combined with accurate temperature/pressure evaluations for thermodynamic and kinetic properties of biological systems2021
- Author(s)
  Jaewoon Jung, 笠原健人, 小林千草, 尾嶋拓, 森貴治, 杉田有治
- Organizer
  第 35 回分子シミュレーション討論会
- Data Source
  KAKENHI-PROJECT-19H05645
[Presentation] スーパーコンピュータが明らかにする蛋白質の動的構造と機能2020
- Author(s)
  杉田有治
- Organizer
  理研・東北大学連携シンポジウム「計測科学が拓く生命科学の新展開」
- Invited
- Data Source
  KAKENHI-PROJECT-19H05645
[Presentation] 計算機シミュレーションで細胞の中を観る2020
- Author(s)
  杉田有治
- Organizer
  京都大学MACSコロキアム
- Invited
- Data Source
  KAKENHI-PROJECT-19H05645
[Presentation] Reduced protein-protein interactions in the cellular crowding with binding of nucleoside triphosphates2020
- Author(s)
  優乙石, Michael Feig, 杉田有治
- Organizer
  第58回生物物理学会年会
- Data Source
  KAKENHI-PROJECT-19H05645
[Presentation] 細胞環境はどのようにタンパク質の構造・ダイナミクス・機能に影響を与えるか？2020
- Author(s)
  杉田有治
- Organizer
  CBI学会2020年大会
- Invited
- Data Source
  KAKENHI-PROJECT-19H05645
[Presentation] All-atom molecular dynamics simulations of spike protein on the surface of SARS-CoV-2 in solution2020
- Author(s)
  Yuji Sugita
- Organizer
  RIKEN-NRC HPC Workshop
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-19H05645
[Presentation] 新型コロナウイルス表面のタンパク質動的構造予測2020
- Author(s)
  杉田有治
- Organizer
  第9回JCAHPCセミナー
- Invited
- Data Source
  KAKENHI-PROJECT-19H05645
[Presentation] Use of enhanced conformational sampling for the analysis of protein-ligand binding processes2020
- Author(s)
  Yuji Sugita
- Organizer
  Telluride Summer Research Conference
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-19H05645
[Presentation] Free-Energy Calculations of Protein-Ligand Binding by Enhanced Sampling Methods2019
- Author(s)
  Yuji Sugita
- Organizer
  The 10th Toyota RIKEN International Workshop on Science of Life Phenomena Woven by Water and Biomolecules
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-19H05645
[Presentation] スパコン「京」とGENESISを用いた創薬自由エネルギー計算2019
- Author(s)
  杉田有治, 李秀栄
- Organizer
  第4回理研ー製薬協連携フォーラム「創薬専用MDシミュレーターの産学共同開発」
- Invited
- Data Source
  KAKENHI-PROJECT-19H05645
[Presentation] Free-Energy Landscape of Protein-Ligand Binding by generalized REST2019
- Author(s)
  Yuji Sugita
- Organizer
  257th ACS national meeting
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-19H05645
[Presentation] 分子動力学で見る細胞質内での分子の動き2019
- Author(s)
  杉田有治
- Organizer
  Chemical Probe第二回合同合宿セミナー
- Invited
- Data Source
  KAKENHI-PROJECT-19H05645
[Presentation] Simulations of Biomolecules in Cellular Crowded Environments2019
- Author(s)
  Yuji Sugita
- Organizer
  Albany 2019. the 20th Conversation
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-19H05645
[Presentation] Large-scale molecular dynamics simulation of biomolecules in cellular environments2019
- Author(s)
  Yuji Sugita
- Organizer
  Accelerated Data Analytics and Computing Workshop 8
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-19H05645
[Presentation] Free-Energy Calculations of Protein-Ligand Binding in Solution and in Cellular Environments2019
- Author(s)
  Yuji Sugita
- Organizer
  Free Energy Workshop
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-19H05645
[Presentation] Slow-down of protein and metabolite diffusion in crowded protein solution", TSRC workshop on macromolecular crowding2019
- Author(s)
  Yuji Sugita
- Organizer
  Telluride Summer Conference
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-19H05645
[Presentation] Molecular Dynamics and Interaction of Protein-Ligand Binding in Crowded Cellular Environments2019
- Author(s)
  Yuji Sugita
- Organizer
  the 42th Annual Meeting of the Molecular Biology Society of Japan
- Invited
- Data Source
  KAKENHI-PROJECT-19H05645
[Presentation] Protein-protein and protein-ligand interaction in cellular environments2019
- Author(s)
  Yuji Sugita
- Organizer
  PSSJ 19th Annual Symposium
- Invited
- Data Source
  KAKENHI-PROJECT-19H05645
[Presentation] Machine learning approach to link MD simulation with single-molecule experiment for understanding protein folding and dynamics2019
- Author(s)
  Yuji Sugita
- Organizer
  The 5th Korean-Polish Conference on "Protein Folding: Theoretical and Experimental Approaches
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-19H05645
[Presentation] Enhanced Conformational Sampling Methods for Free Energy Calculation2019
- Author(s)
  Yuji Sugita
- Organizer
  CHARMM-GUI Workshop
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-19H05645
[Presentation] Free-Energy Calculations of Protein-Ligand Binding using GENESIS2019
- Author(s)
  Yuji Sugita
- Organizer
  Supercomputer Symposium at IMS
- Invited
- Data Source
  KAKENHI-PROJECT-19H05645
[Presentation] Free-Energy Calculations of Protein-Ligand Binding using GENESIS software2019
- Author(s)
  Yuji Sugita
- Organizer
  ICMS2019
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-19H05645
[Presentation] Protein-Drug Interaction in Dilute Solution and in Cellular Environments2018
- Author(s)
  Yuji Sugita
- Organizer
  The XIV-th ICISE Workshop on Computational Biophysics at the Molecular and Meso Scales
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-26119006
[Presentation] Data-driven molecular simulations for integrative dynamic structural biology2018
- Author(s)
  Yuji Sugita and Yasuhiro Matsunaga
- Organizer
  Second workshop on Advances in Theory and Computation of Complex Systems - Biological Systems.
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-26119006
[Presentation] Conformational changes between E1P and E2P states of SERCA by MD simulations based on string method and free-energy calculations2018
- Author(s)
  Yuji Sugita
- Organizer
  Symposium on “Membrane Protein Simulations and Free Energy Approaches” in the 256th ACS National Meeting in Boston
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-26119006
[Presentation] Optimization and Parallelization of GENESIS on GPU platforms2018
- Author(s)
  Yuji Sugita
- Organizer
  International Workshop on GPU accelerated Molecular Dynamics Simulations
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-26119006
[Presentation] Mechanisms for Protein-Ligand Binding in Solution and in Cellular Environments2018
- Author(s)
  Yuji Sugita
- Organizer
  The 18th KIAS conference on Protein Structure and Function
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-26119006
[Presentation] Molecular Simulations for Understanding Protein Functions in Cellular Environments2018
- Author(s)
  Yuji Sugita
- Organizer
  The 41st Annual Meeting of the Molecular Biology Society of Japan
- Invited
- Data Source
  KAKENHI-PLANNED-26119006
[Presentation] Development of the flexible-fitting MD simulation method for cryo-EM images of large macromolecular structures and dynamics2018
- Author(s)
  Yuji Sugita
- Organizer
  Symposium on “COMP Meets CRYO: New Frontiers in Flexible Fitting, Image Processing & Refinement of Cryo-EM Data” in in the 256th ACS National Meeting in Boston
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-26119006
[Presentation] 分子動力学ソフトウェアGENESISの開発と細胞内分子ダイナミクスのシミュレーション2017
- Author(s)
  杉田有治
- Organizer
  第９回シグナルネットワーク研究会
- Invited
- Data Source
  KAKENHI-PLANNED-26119006
[Presentation] バクテリア細胞質の全原子分子動力学シミュレーションによる分子ダイナミクスの解析2017
- Author(s)
  杉田有治
- Organizer
  第4回森野ディスカッション
- Invited
- Data Source
  KAKENHI-PLANNED-26119006
[Presentation] Molecular Dynamics Simulations of Conformational Changes in SR Ca2+-ATPase2017
- Author(s)
  Yuji Sugita
- Organizer
  P-type ATPase Meeting 2017
- Invited
- Data Source
  KAKENHI-PLANNED-26119006
[Presentation] Machine Learning Approach for Protein Dynamics by combining smFRET and MD simulations2017
- Author(s)
  杉田有治
- Organizer
  Telluride Summer Conference on Free Energy Calculations: Three decades of adventure in chemistry and biophysics
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-26119006
[Presentation] Rapid Nitric Oxide Transport in the Nitrite Reductase:Nitric Oxide Reductase Complex2017
- Author(s)
  Yuji Sugita
- Organizer
  The 1st Samsung Global Research Symposium on “Structure Dynamics, and Thermodynamics of Biomolecular Networks”
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-26119006
[Presentation] Experimental and Computational Analysis of Protein-Protein Interaction in Cellular Environments2017
- Author(s)
  杉田有治
- Organizer
  生物物理学会年会
- Invited
- Data Source
  KAKENHI-PLANNED-26119006
[Presentation] 動的構造と生体環境を考慮した創薬応用シミュレーション2017
- Author(s)
  杉田有治
- Organizer
  CBI学会
- Invited
- Data Source
  KAKENHI-PLANNED-26119006
[Presentation] 分子動力学を用いた細胞内分子動態の解析2017
- Author(s)
  杉田有治
- Organizer
  構造活性相関シンポジウム
- Invited
- Data Source
  KAKENHI-PLANNED-26119006
[Presentation] Molecular dynamics simulations on biomolecular-structure-dynamics-function relationship in cellular environments2017
- Author(s)
  杉田有治
- Organizer
  第17回日本蛋白質科学会年会
- Invited
- Data Source
  KAKENHI-PLANNED-26119006
[Presentation] 2.Recent development of replica-exchange molecular dynamics simulation methods2016
- Author(s)
  Yuji Sugita
- Organizer
  251st ACS national meeting & exposition
- Place of Presentation
  San Diego, USA
- Year and Date
  2016-03-16
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-26119006
[Presentation] Enhanced conformational sampling methods for conformational dynamics of proteins, membranes, and N-glycans2016
- Author(s)
  Yuji Sugita
- Organizer
  International Workshop on Frontiers in Molecular Biophysics
- Place of Presentation
  Shanghai・China
- Year and Date
  2016-07-23
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-26119006
[Presentation] Two-Step Proton Transfer Mechanisms in the Outward-Facing Form of MATE Multidrug Transporter2016
- Author(s)
  Yuji Sugita
- Organizer
  IAS Focused Program on Molecular Machines of Life: Simulation Meets Experiment
- Place of Presentation
  Hong Kong・China
- Year and Date
  2016-05-26
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-26119006
[Presentation] 細胞環境における蛋白質の動態解析のためのNMRおよび計算科学的アプローチ2016
- Author(s)
  白川昌宏，杉田有治
- Organizer
  シンポジウム「細胞環境における蛋白質の動態解析のためのNMRおよび計算科学的アプローチ」
- Place of Presentation
  京都市　京都大学
- Year and Date
  2016-03-28
- Data Source
  KAKENHI-ORGANIZER-26119001
[Presentation] Ion mobility spectrometry separation of isomeric N-glycan structures2016
- Author(s)
  Yamaguchi Y, Hirose K, Nishima W, Re S, Sugita Y
- Organizer
  RIKEN-Max Planck Joint Research Center for Systems Chemical Biology ５th Annual Symposium
- Place of Presentation
  Berlin, Germany
- Year and Date
  2016-04-18
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-25460054
[Presentation] In-vivo macromolecular crowding effects2016
- Author(s)
  Yuji Sugita
- Organizer
  Telluride Summer Conference
- Place of Presentation
  Telluride Colorado・USA
- Year and Date
  2016-06-27
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-26119006
[Presentation] 細胞内分子ダイナミクスを理解するために必要なシミュレーションと放射光生命科学2016
- Author(s)
  杉田有治
- Organizer
  第29回日本放射光学年会放射光科学合同シンポジウム
- Place of Presentation
  柏の葉カンファレンスセンター, 千葉県柏市
- Year and Date
  2016-01-11
- Invited
- Data Source
  KAKENHI-PLANNED-26119006
[Presentation] Enhanced conformational sampling methods for membrane protein folding and dynamics2016
- Author(s)
  Yuji Sugita
- Organizer
  4th International Conference on Molecular Simulations 2016 (ICMS2016)
- Place of Presentation
  Shanghai・China
- Year and Date
  2016-10-25
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-26119006
[Presentation] 7.Role of lipid molecules on molecular functions of membrane proteins2015
- Author(s)
  Yuji Sugita
- Organizer
  第53回日本生物物理学会年会
- Place of Presentation
  金沢大学、石川県金沢市
- Year and Date
  2015-09-13
- Invited
- Data Source
  KAKENHI-PLANNED-26119006
[Presentation] レプリカ交換分子動力学計算による糖鎖イオン移動度質量スペクトルの予測2015
- Author(s)
  李秀栄、渡部茂久、二島渉、宗行英朗、山口芳樹、杉田有治
- Organizer
  第1回理化学研究所・産業技術総合研究所共同シンポジウム「ビッグデータとビッグシミュレーションによる生命医科学の未来」
- Place of Presentation
  産業技術総合研究所（東京都、江東区）
- Year and Date
  2015-06-29
- Data Source
  KAKENHI-PROJECT-25330358
[Presentation] 膜輸送タンパク質におけるプロトン対抗輸送の役割2015
- Author(s)
  杉田有治
- Organizer
  分子研研究会「膜タンパク質内部のプロトン透過を考える」
- Place of Presentation
  分子科学研究所、愛知県岡崎市
- Year and Date
  2015-04-21
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-26119006
[Presentation] 9.Parallel MD simulations for enhanced conformational sampling of biological systems2015
- Author(s)
  Yuji Sugita
- Organizer
  The 8th International Congress on Industrial and Applied Mathematics
- Place of Presentation
  Beijing, China
- Year and Date
  2015-08-19
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-26119006
[Presentation] 5.Free-energy calculations of conformational changes in membrane proteins by multi-resolution methods2015
- Author(s)
  Yuji Sugita
- Organizer
  The 25th Hot Spring Harbor International Symposium
- Place of Presentation
  九州大学, 福岡県福岡市
- Year and Date
  2015-11-14
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-26119006
[Presentation] 4.Role of lipid molecules on the proton antiproton in MATE multi drug transporter, 杉田有治, BMB20152015
- Author(s)
  杉田有治
- Organizer
  第38回日本分子生物学会年会、第88回日本生化学会大会合同大会
- Place of Presentation
  神戸ポートアイランド, 兵庫県神戸市
- Year and Date
  2015-12-02
- Invited
- Data Source
  KAKENHI-PLANNED-26119006
[Presentation] Hydration structure at ceramide/water interface: A molecular dynamics simulation study.2015
- Author(s)
  Suyong Re, Wataru Nishima, Tahei Tahara, Yuji Sugita
- Organizer
  第53回日本生物物理学会年会
- Place of Presentation
  金沢大学（石川県、金沢市）
- Year and Date
  2015-09-13
- Data Source
  KAKENHI-PROJECT-25330358
[Presentation] Modeling the MAPK/ERK pathway under crowding environment by the combined multi-scale simulations.2015
- Author(s)
  Suyong Re, Po-Hung Wang, Isseki Yu, and Yuji Sugita
- Organizer
  Supercomputational Life Science 2015 (SCLS2015)
- Place of Presentation
  東京大学（東京都、文京区）
- Year and Date
  2015-10-20
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-25330358
[Presentation] 分子動力学計算の高速化と大規模生体分子シミュレーション2014
- Author(s)
  杉田有治
- Organizer
  バイオスーパーコンピューティング研究会2014(第6回)総会・講演会
- Place of Presentation
  理研, 埼玉県和光市広沢
- Year and Date
  2014-10-15
- Invited
- Data Source
  KAKENHI-PLANNED-26119006
[Presentation] 理論・計算化学に基づく脂質ダイナミクスの解析2014
- Author(s)
  杉田有治
- Organizer
  第87回日本生化学会大会
- Place of Presentation
  京都国際会議場, 京都市左京区
- Year and Date
  2014-10-17
- Invited
- Data Source
  KAKENHI-PLANNED-26119006
[Presentation] REMD-based prediction of structure and function of glycans」新学術領域「動的秩序と機能2014
- Author(s)
  李秀栄, 二島渉, 渡部茂久, 杉田有治
- Organizer
  第2回国際シンポジウム
- Place of Presentation
  京都
- Year and Date
  2014-01-12
- Data Source
  KAKENHI-PROJECT-25540138
[Presentation] REMD-based prediction of structure and function of glycans2014
- Author(s)
  李秀栄、二島渉、渡部茂久、杉田有治
- Organizer
  新学術領域「動的秩序と機能」第２回国際シンポジウム
- Place of Presentation
  キャンパスプラザ京都（京都）
- Data Source
  KAKENHI-PROJECT-25330358
[Presentation] 細胞内環境での蛋白質の運動と分子認識2014
- Author(s)
  杉田有治
- Organizer
  CBI研究会
- Place of Presentation
  東京大学山上会館
- Invited
- Data Source
  KAKENHI-PUBLICLY-24121726
[Presentation] 糖鎖の化学シフト計算と立体構造予測への応用2013
- Author(s)
  李秀栄, 山口芳樹, 杉田有治
- Organizer
  第7回分子科学討論会
- Place of Presentation
  京都
- Year and Date
  2013-09-27
- Data Source
  KAKENHI-PROJECT-25540138
[Presentation] Revised CHARMM carbohydrate force field for improved description of conformational diversity of N-glycans2013
- Author(s)
  李秀栄, 渡部茂久, 二島渉, 杉田有治
- Organizer
  第51回日本生物物理学会年会
- Place of Presentation
  京都
- Year and Date
  2013-10-30
- Data Source
  KAKENHI-PROJECT-25540138
[Presentation] レプリカ交換分子動力学計算によるPA 化糖鎖の立体構造解析2013
- Author(s)
  渡部茂久, 李秀栄, 宗行英朗, 杉田有治
- Organizer
  第51回日本生物物理学会年会
- Place of Presentation
  京都
- Year and Date
  2013-10-30
- Data Source
  KAKENHI-PROJECT-25540138
[Presentation] 糖鎖の化学シフト計算と立体構造予測への応用2013
- Author(s)
  李秀栄、山口芳樹、杉田有治
- Organizer
  第７回分子科学討論会
- Place of Presentation
  京都テルサ
- Data Source
  KAKENHI-PROJECT-25540138
[Presentation] Prediction of Structure and Dynamics of Glycans from Molecular Dynamics Simulations.2013
- Author(s)
  李秀栄、二島渉、渡部茂久、杉田有治
- Organizer
  3rd International Conference on Molecular Simulation (ICMS2013)
- Place of Presentation
  神戸国際会議場（神戸）
- Data Source
  KAKENHI-PROJECT-25540138
[Presentation] Conformational analysis of PA-glycans by replica-exchange molecular dynamics simulation2013
- Author(s)
  渡部茂久, 李秀栄, 二島渉, 宗行英朗, 杉田有治
- Place of Presentation
  神戸
- Year and Date
  2013-11-18
- Data Source
  KAKENHI-PROJECT-25540138
[Presentation] 糖鎖の化学シフト計算と立体構造予測への応用2013
- Author(s)
  李秀栄、山口芳樹、杉田有治
- Organizer
  第７回分子科学討論会
- Place of Presentation
  京都テルサ（京都）
- Data Source
  KAKENHI-PROJECT-25330358
[Presentation] Revised CHARMM carbohydrate force field for improved description of conformational diversity of N-glycans2013
- Author(s)
  李秀栄、渡部茂久、二島渉、杉田有治
- Organizer
  第５１回日本生物物理学会年会
- Place of Presentation
  国立京都国際会館（京都）
- Data Source
  KAKENHI-PROJECT-25540138
[Presentation] Revised CHARMM carbohydrate force field for improved description of conformational diversity of N-glycans2013
- Author(s)
  李秀栄、渡部茂久、二島渉、杉田有治
- Organizer
  第５１回日本生物物理学会年会
- Place of Presentation
  国立京都国際会館（京都）
- Data Source
  KAKENHI-PROJECT-25330358
[Presentation] Conformational analysis of PA-glycans by replica-exchange molecular dynamics simulation.2013
- Author(s)
  渡部茂久、李秀栄、二島渉、宗行英朗、杉田有治
- Organizer
  3rd International Conference on Molecular Simulation (ICMS2013)
- Place of Presentation
  神戸国際会議場（神戸）
- Data Source
  KAKENHI-PROJECT-25330358
[Presentation] レプリカ交換分子動力学計算によるPA化糖鎖の立体構造解析2013
- Author(s)
  渡部茂久、李秀栄、宗行英朗、杉田有治
- Organizer
  第５１回日本生物物理学会年会
- Place of Presentation
  国立京都国際会館（京都）
- Data Source
  KAKENHI-PROJECT-25330358
[Presentation] Prediction of Structure and Dynamics of Glycans from Molecular Dynamics Simulations.2013
- Author(s)
  李秀栄、二島渉、渡部茂久、杉田有治
- Organizer
  3rd International Conference on Molecular Simulation (ICMS2013)
- Place of Presentation
  神戸国際会議場（神戸）
- Data Source
  KAKENHI-PROJECT-25330358
[Presentation] Prediction of Structure and Dynamics of Glycans from Molecular Dynamics Simulations2013
- Author(s)
  李秀栄, 二島渉, 渡部茂久, 杉田有治
- Organizer
  3rd International Conference on Molecular Simulation (ICMS2013)
- Place of Presentation
  神戸
- Year and Date
  2013-11-20
- Data Source
  KAKENHI-PROJECT-25540138
[Presentation] レプリカ交換分子動力学シミュレーションによる水中N型糖鎖の構造多様性とその調節機構の研究2011
- Author(s)
  二島渉、宮下尚之、山口芳樹、杉田有治、李秀栄
- Organizer
  第25回分子シミュレーション討論会
- Place of Presentation
  東京
- Year and Date
  2011-12-05
- Data Source
  KAKENHI-PUBLICLY-22121521
[Presentation] ミトコンドリアへの輸送蛋白質に付加されたプレ配列認識モデルの分子動力学計算による検証2011
- Author(s)
  小室靖明、森貫治、宗行英朗、齊藤貫士、神田大輔、杉田有治
- Organizer
  第25回分子シミュレーション討論会
- Place of Presentation
  東京
- Year and Date
  2011-12-05
- Data Source
  KAKENHI-PUBLICLY-22121521
[Presentation] Prediction of dynamical conformation of biantennary complex-type N-glycan in water by replica-exchange molecular dynamics simulations2011
- Author(s)
  李秀栄、宮下尚之、山口芳樹、杉田有治
- Organizer
  第49回日本生物物理学会年会
- Place of Presentation
  兵庫
- Year and Date
  2011-09-18
- Data Source
  KAKENHI-PUBLICLY-22121521
[Presentation] Molecular dynamics simulation of outer mitochondrial membrane protein Tom20-presequence complex2011
- Author(s)
  小室靖明,森貴治、宗行英朗、齊藤貴士、神田大輔、杉田有治
- Organizer
  第49回日本生物物理学会年会
- Place of Presentation
  兵庫
- Year and Date
  2011-09-18
- Data Source
  KAKENHI-PUBLICLY-22121521
[Presentation] All-atom molecular dynamics simulations of the Sec translocon in biological membrane2010
- Author(s)
  Yuji Sugita
- Organizer
  第33回日本分子生物物理学会年会
- Place of Presentation
  ポートピアホテル、神戸
- Year and Date
  2010-12-09
- Data Source
  KAKENHI-PUBLICLY-22121521
[Presentation] Soft interactions between calcium pump (SERCA) and phospholamban (PLN)2010
- Author(s)
  杉田有治
- Organizer
  第48回日本生物物理学会年会
- Place of Presentation
  東北大学川内キャンパス、仙台
- Year and Date
  2010-09-21
- Data Source
  KAKENHI-PUBLICLY-22121521
[Presentation] Replica-exchange molecular dynamics simulations of proteins in solution and in biological membrane2010
- Author(s)
  Yuji Sugita
- Organizer
  Telluride Summer Conference on "Protein and Peptide Interactions in Cellular Environments"
- Place of Presentation
  Telluride, Colorado, USA
- Year and Date
  2010-07-20
- Data Source
  KAKENHI-PUBLICLY-22121521
[Presentation] 生体膜と膜蛋白質の分子動力学計算2010
- Author(s)
  杉田有治
- Organizer
  第10回日本蛋白質科学会年会
- Place of Presentation
  札幌コンベンションセンター、札幌
- Year and Date
  2010-06-18
- Data Source
  KAKENHI-PUBLICLY-22121521
[Presentation] Replica-exchange molecular dynamics simulations of proteins in solution and in biological membrane2010
- Author(s)
  Yuji Sugita
- Organizer
  The 10^<th> KIAS Conference on Protein Structure and Function
- Place of Presentation
  KIAS, Seoul, Korea
- Year and Date
  2010-10-02
- Data Source
  KAKENHI-PUBLICLY-22121521
[Presentation] Molecular Dynamics Simulations of Soft Interactions at the Membrane Interface2009
- Author(s)
  杉田有治
- Organizer
  International Symposium on Molecular Soft Interactions in Biological Systems
- Place of Presentation
  大阪
- Data Source
  KAKENHI-PROJECT-15083201
[Presentation] 膜蛋白質の分子動力学計算2009
- Author(s)
  杉田有治
- Organizer
  計算科学研究センター・ワークショップ
- Place of Presentation
  岡崎
- Data Source
  KAKENHI-PROJECT-15083201
[Presentation] Molecular Dynamics Study of Sarcoplasmic Reticulum Calcium Pump2008
- Author(s)
  Yuji Sugita
- Organizer
  第31回日本分子生物学会年会・第81回日本生化学会大会 (BMB2008)
- Place of Presentation
  神戸
- Data Source
  KAKENHI-PROJECT-15083201
[Presentation] Toward a complete understanding of molecular mechanism of ion transport by membrane proteins2008
- Author(s)
  Yuji Sugita
- Organizer
  1st Joint Workshop on Computational Science
- Place of Presentation
  和光
- Data Source
  KAKENHI-PROJECT-15083201
[Presentation] カルシウムポンプの機能発現機構に関する分子動力学計算2008
- Author(s)
  杉田有治
- Organizer
  日本物理学会第63回年次大会
- Place of Presentation
  東大阪
- Data Source
  KAKENHI-PROJECT-15083201
[Presentation] 分子シミュレーションからカルシウムポンプの構造柔軟性を考える2008
- Author(s)
  杉田有治
- Organizer
  日本生物物理学会
- Place of Presentation
  パシフィコ横浜
- Year and Date
  2008-12-22
- Data Source
  KAKENHI-PROJECT-15083201
[Presentation] Protein-Lipid Interactions Revealed by Molecular Dynamics Simulations2008
- Author(s)
  杉田有治
- Organizer
  九州大学次世代研究スーパースター養成プログラム公開シンポジウム
- Place of Presentation
  博多
- Data Source
  KAKENHI-PROJECT-15083201
[Presentation] Molecular mechanism for stabilizing Ca^<2+> at the transmembrane binding sites in Ca^<2+>-pump2008
- Author(s)
  Yuji Sugita
- Organizer
  1st CMD International Symposium Chemical Computations
- Place of Presentation
  Seoul
- Data Source
  KAKENHI-PROJECT-15083201
[Presentation] Molecular Dynamics Study of Sarcoplasmic Reticulum Calcium Pump2008
- Author(s)
  杉田有治
- Organizer
  第31回日本分子生物学会・第81回日本生化学会合同大会
- Place of Presentation
  神戸ポートピアホテル
- Year and Date
  2008-12-09
- Data Source
  KAKENHI-PROJECT-15083201
[Presentation] Molecular Dynamics simulations of protein dynamics in biological membrane2008
- Author(s)
  杉田有治
- Organizer
  次世代ナノ情報機能・材料グループ成果報告会
- Place of Presentation
  仙台
- Data Source
  KAKENHI-PROJECT-15083201
[Presentation] Molecular Dynamics Simulations on the Conformational Stability of the Ca^<2+>-binding sites in Ca^<2+>-pump2007
- Author(s)
  Yuji Sugita
- Organizer
  BNL-RIKEN Life Science Workshop
- Place of Presentation
  Upton
- Data Source
  KAKENHI-PROJECT-15083201
[Presentation] 分子シミュレーションからカルシウムポンプの構造柔軟性を考える2007
- Author(s)
  杉田有治
- Organizer
  日本生物物理学会第45回年会
- Place of Presentation
  横浜
- Data Source
  KAKENHI-PROJECT-15083201
[Presentation] カルシウムポンプによるイオン能動輸送の分子機構2007
- Author(s)
  杉田有治
- Organizer
  理研シンポジウム「計算機と生物学 in Silico Biology」
- Place of Presentation
  和光
- Data Source
  KAKENHI-PROJECT-15083201
[Presentation] カルシウムポンプとその阻害剤の分子動力学計算2006
- Author(s)
  杉田有治
- Organizer
  スーパーコンピュータワークショップ
- Place of Presentation
  自然科学機構・岡崎共通研究施設・計算科学研究センター
- Data Source
  KAKENHI-PROJECT-15083201
[Presentation] カルシウムポンプの分子動力学計算 : 構造から機能の理解へ2006
- Author(s)
  杉田有治
- Organizer
  京都大学ウイルス研セミナー
- Place of Presentation
  京都大学ウイルス研究所
- Data Source
  KAKENHI-PROJECT-15083201
[Presentation] 分子動力学計算によるカルシウムポンプの機能制御機構の解析2006
- Author(s)
  杉田有治
- Organizer
  大阪大学蛋白研セミナー
- Place of Presentation
  大阪大学蛋白質研究所
- Data Source
  KAKENHI-PROJECT-15083201
[Presentation] レプリカ交換法による蛋白質機能解析2006
- Author(s)
  杉田有治
- Organizer
  第6回蛋白質科学会年会
- Place of Presentation
  京都国際会議場
- Year and Date
  2006-04-26
- Data Source
  KAKENHI-PROJECT-15083201
[Presentation] Molecular dynamics simulations of sarcoplasimc reticulum calcium pump in membrane2006
- Author(s)
  Yuji Sugita
- Organizer
  In Satellite meeting for 20^<th> IUBMB International Congress of Biochemistry and Molecular Biology & 11^<th> FAOBMB Congress on Molecular Mechanism and Regulation in Cation Transport ATPases and Related Genetic Diseases
- Place of Presentation
  京都リサーチパーク
- Data Source
  KAKENHI-PROJECT-15083201
[Presentation] Theoretical studies on the proton countertransport by sarcoplasmic reticulum calcium pump2006
- Author(s)
  Yuji Sugita
- Organizer
  In KAIST seminar
- Place of Presentation
  KAIST、Korea
- Data Source
  KAKENHI-PROJECT-15083201
[Presentation] SR Ca^<2+>-ATPaseによるCa^<2+>輸送とプロトン対抗輸送の分子機構2006
- Author(s)
  杉田有治
- Organizer
  第4回特定領域研究「膜インターフェイス」公開シンポジウム
- Place of Presentation
  京都大学百周年記念ホール
- Year and Date
  2006-07-05
- Data Source
  KAKENHI-PROJECT-15083201
[Presentation] 分子動力学計算による蛋白質原子揺らぎの収束性について2006
- Author(s)
  杉田有治
- Organizer
  大阪大学蛋白研セミナー
- Place of Presentation
  大阪大学蛋白質研究所
- Data Source
  KAKENHI-PROJECT-15083201
[Presentation] SR Ca^<2+>-ATPase Atomic Structure and Molecular Dynamics Simulations2005
- Author(s)
  Yuji Sugita, Chikashi Toyoshima
- Organizer
  In 11-th International ATPase Conference and 59-th Annual Meeting and Symposium of the Society of General Physiologists
- Place of Presentation
  Marine Biological Laboratory, Woods Hole, Massachusetts
- Data Source
  KAKENHI-PROJECT-15083201
[Presentation] 筋小胞体Ca^<2+>-ATPaseの機能に関する分子動力学計算2005
- Author(s)
  杉田有治
- Organizer
  第28回日本分子生物学会年会
- Place of Presentation
  福岡ドーム
- Data Source
  KAKENHI-PROJECT-15083201
[Presentation] Molecular dynamics studies on the biological functions of sarcoplasmic reticulum Ca^<2+>-ATPase.2005
- Author(s)
  Yuji Sugita
- Organizer
  In P-Chem seminar
- Place of Presentation
  Boston University、Boston
- Data Source
  KAKENHI-PROJECT-15083201
[Presentation] Molecular dynamics studies on Sarcoplasmic reticulum Ca^<2+>-ATPase2005
- Author(s)
  Yuji Sugita
- Organizer
  In Theoretical Biophysics Seminar
- Place of Presentation
  Rutgars University, New Jersey
- Data Source
  KAKENHI-PROJECT-15083201
[Presentation] Molecular dynamics simulations SR Ca^<2+>-ATPase in the Ca^<2+>-bound and unbound states2005
- Author(s)
  Yuji Sugita, Chikashi Toyoshima
- Organizer
  In 2005 FASEB Summer Research Conferences
- Place of Presentation
  Vermont Academy, Saxton River, Vermont, USA
- Data Source
  KAKENHI-PROJECT-15083201
[Presentation] Molecular Mechanism of cooperative Ca^<2+>-binding by Ca2+-ATPase, insight from molecular dynamics simulations2005
- Author(s)
  Yuji Sugita
- Organizer
  In the 2^<nd> symposium of membrane interface
- Place of Presentation
  ホテル阪急エキスポパーク
- Data Source
  KAKENHI-PROJECT-15083201
[Presentation] 脂質二重膜中におけるカルシウムポンプの運動と機能2005
- Author(s)
  杉田有治
- Organizer
  生体分子ダイナミックス研究会
- Place of Presentation
  東京大学農学部
- Data Source
  KAKENHI-PROJECT-15083201
[Presentation] 脂質二重膜中でのカルシウムポンプの分子動力学2004
- Author(s)
  杉田有治
- Organizer
  第1回特定領域研究「膜インターフェイス」公開シンポジウム
- Place of Presentation
  東京大学山上会館
- Data Source
  KAKENHI-PROJECT-15083201
[Presentation] Domain motion analysis of membrane proteins by bioinformatics and molecular dynamics simulations
- Author(s)
  Yuji Sugita
- Organizer
  The international workshop on computational science and engineering
- Place of Presentation
  Hong Kong City University, Hong Kong
- Year and Date
  2014-12-13 – 2014-12-16
- Invited
- Data Source
  KAKENHI-PLANNED-26119006
[Presentation] Confident Identification of Isomeric N-glycan Structures by Combined Ion Mobility Mass Spectrometry and Hydrophilic Interaction Liquid Chromatograph
- Author(s)
  Y. Yamaguchi, K. Hirose, W. Nishima, S. Re and Y. Sugita
- Organizer
  American Society for Mass Spectrometry (ASMS)
- Place of Presentation
  Minneapolis, USA
- Data Source
  KAKENHI-PROJECT-25460054
[Presentation] レプリカ交換分子動力学計算を用いた糖鎖イオンモビリティー質量スペクトルの予測
- Author(s)
  李秀栄、渡部茂久、二島渉、山口芳樹、杉田有治
- Organizer
  第３３回日本糖質学会年会
- Place of Presentation
  名古屋大学豊田講堂（名古屋）
- Year and Date
  2014-08-10 – 2014-08-12
- Data Source
  KAKENHI-PROJECT-25330358
[Presentation] 分子動力学シミュレーションによるN型糖鎖衝突断面積の計算
- Author(s)
  李秀栄、渡部茂久、二島渉、宗行英朗、山口芳樹、杉田有治
- Organizer
  第34回日本糖質学会年会
- Place of Presentation
  東京大学安田講堂（東京）
- Year and Date
  2015-07-31 – 2015-08-02
- Data Source
  KAKENHI-PROJECT-25330358
[Presentation] Structure and orientation of hydrating water molecules at phospholipid/water interface revealed by molecular dynamics simulation.
- Author(s)
  李秀栄、二島渉、田原太平、杉田有治
- Organizer
  第52回日本生物物理学会年会
- Place of Presentation
  札幌コンベンションセンター（札幌）
- Year and Date
  2014-09-25 – 2014-09-27
- Data Source
  KAKENHI-PROJECT-25330358
[Presentation] Domain motion analysis of proteins based on multiple atomic structures and coarse-grained molecular dynamics simulations
- Author(s)
  Yuji Sugita
- Organizer
  Telluride Workshop on Coarse-grained modeling of structure and dynamics of biomolecules, Telluride
- Place of Presentation
  Telluride Science Research Center, Telluride, Collorado, USA
- Year and Date
  2014-08-04 – 2014-08-08
- Invited
- Data Source
  KAKENHI-PLANNED-26119006
[Presentation] A mosaic of water orientation structures at a neutral zwitterion lipid/water interface revealed by molecular dynamics simulations.
- Author(s)
  李秀栄、二島渉、田原太平、杉田有治
- Organizer
  5th AICS International Symposium
- Place of Presentation
  理化学研究所計算科学研究機構（神戸）
- Year and Date
  2014-12-08 – 2014-12-09
- Data Source
  KAKENHI-PROJECT-25330358
[Presentation] Experimental and theoretical approaches to understand the conformational differences in isomeric
- Author(s)
  Y. Yamaguchi, K. Matsumoto, K. Hirose, W. Nishima, S. Re, Y. Sugita
- Organizer
  22nd International Symposium on Glycoconjugates
- Place of Presentation
  Dalian, China
- Invited
- Data Source
  KAKENHI-PROJECT-25460054

1. 西田紀貴 (50456183)

# of Collaborated Projects: 4 results

# of Collaborated Products: 0 results
2. RE Suyong (50390670)

# of Collaborated Projects: 3 results

# of Collaborated Products: 31 results
3. YAMAGUCHI Yoshiki (90323451)

# of Collaborated Projects: 3 results

# of Collaborated Products: 9 results
4. Kohda Daisuke (80186618)

# of Collaborated Projects: 3 results

# of Collaborated Products: 1 results
5. 安藤敏夫 (50184320)

# of Collaborated Projects: 3 results

# of Collaborated Products: 0 results
6. 白川昌宏 (00202119)

# of Collaborated Projects: 3 results

# of Collaborated Products: 1 results
7. 塚崎智也 (80436716)

# of Collaborated Projects: 3 results

# of Collaborated Products: 0 results
8. TAMA FLORENCE (20648191)

# of Collaborated Projects: 2 results

# of Collaborated Products: 1 results
9. 稲垣冬彦 (70011757)

# of Collaborated Projects: 2 results

# of Collaborated Products: 0 results
10. KONDOU Youhei (30436604)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
11. Shiro Yoshitsugu (70183051)

# of Collaborated Projects: 1 results

# of Collaborated Products: 1 results
12. HANASHIMA Shinya (50373353)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
13. NAGAE Masamichi (60619873)

# of Collaborated Projects: 1 results

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14. 三好永作 (70148914)

# of Collaborated Projects: 1 results

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15. 茂木孝一 (30304835)

# of Collaborated Projects: 1 results

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16. 酒井嘉子 (40091392)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
17. 豊島近 (70172210)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
18. 津田岳夫 (10345233)

# of Collaborated Projects: 1 results

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19. 木寺詔紀 (00186280)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
20. 鈴木裕 (50183421)

# of Collaborated Projects: 1 results

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21. 澤井仁美 (50584851)

# of Collaborated Projects: 1 results

# of Collaborated Products: 1 results
22. 甲斐荘正恒 (20137029)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
23. 伊藤隆 (80261147)

# of Collaborated Projects: 1 results

# of Collaborated Products: 9 results
24. 優乙石 (90402544)

# of Collaborated Projects: 1 results

# of Collaborated Products: 71 results
25. 吉川雅英 (80272425)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
26. 稲葉謙次 (10423039)

# of Collaborated Projects: 1 results

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27. 水上進 (30420433)

# of Collaborated Projects: 1 results

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28. 田中元雅 (40321781)

# of Collaborated Projects: 1 results

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29. 仁田亮 (40345038)

# of Collaborated Projects: 1 results

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30. 山本林 (80551283)

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31. 倉永英里奈 (90376591)

# of Collaborated Projects: 1 results

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32. 福間剛士 (90452094)

# of Collaborated Projects: 1 results

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33. 笠原健人 (10824469)

# of Collaborated Projects: 1 results

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34. AKUTSU hideo

# of Collaborated Projects: 1 results

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35. SHIMADA ichio

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
36. NISHIMURA yoshifumi

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
37. SUGIMOTO Hiroshi

# of Collaborated Projects: 1 results

# of Collaborated Products: 1 results
38. TOSHA Takehiko

# of Collaborated Projects: 1 results

# of Collaborated Products: 1 results
39. NAKAMURA Hiro

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
40. HISANO Tamao

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
41. KUBO Minoru

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
42. YAGI Kiyoshi

# of Collaborated Projects: 1 results

# of Collaborated Products: 4 results
43. TAKITA Ryo

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results
44. GALVELIS Raimondas

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results
45. MATSUNAGA Yasuhiro

# of Collaborated Projects: 0 results

# of Collaborated Products: 4 results
46. 宮下治

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results
47. 鄭載運

# of Collaborated Projects: 0 results

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48. 田原太平

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results
49. 森貴治

# of Collaborated Projects: 0 results

# of Collaborated Products: 5 results
50. 森本雄祐

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results
51. 宮下尚之

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results

SUGITA Yuji 杉田 有治

杉田 有冶 スギタ ユウジ

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Cross-scale data-driven modeling of biomolecular dynamics in the cellsPrincipal Investigator

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Multi-scale molecular dynamics simulation on biomolecular dynamics in crowded cellular environmentsPrincipal Investigator

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Molecular dynamics simulations of protein complexes based on multi-resolution modelsPrincipal Investigator

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Prediction of Protein-Glycan Structure Complex with Low Binding AffinityPrincipal Investigator

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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Principal Investigator

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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Principal Investigator

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Molecular dynamics simulations on membrane transporting proteinsPrincipal Investigator

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SUGITA Yuji 杉田有治

杉田有冶スギタユウジ