Yu Isseki 優乙石

… Alternative Names

優乙石ユウイッセキ

YU Isseki 優乙石

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Researcher Number	90402544
Affiliation (Current)	2025: 前橋工科大学, 工学部, 准教授
Affiliation (based on the past Project Information) *help	2019 – 2023: 前橋工科大学, 工学部, 准教授 2015 – 2016: 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, 研究員 2014: 独立行政法人理化学研究所, 杉田理論分子科学研究室, 研究員 2013: 独立行政法人理化学研究所, 杉田理論分子科学研究室, 協力研究員 2008 – 2012: Aoyama Gakuin University, 理工学部, 助教 2007: Nagoya University, 大学院・工学研究科, COE研究員
Review Section/Research Field	Principal Investigator Physical chemistry / Basic Section 32010:Fundamental physical chemistry-related Except Principal Investigator Broad Section G
Keywords	Principal Investigator 分子動力学 / 分子混雑 / 細胞環境 / 水和 / 蛋白質 / 生物物理 / 蛋白質間相互作用 / ATP / 分子動力学シミュレーション / 深海 … More / 部分モル体積 / 高圧 / ハイパフォーマンスコンピューティング / TMAO / オスモライト / 自由エネルギー / 分子クラウディング / 理論化学 / 計算化学 / Kirkwood-Buff理論 / 選択的水和 / 溶媒効果 / エクトイン / タンパク質 … More Except Principal Investigator 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 / 細胞内環境 / 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 / 分子動力学 Less

Multi-scale molecular dynamics simulation on biomolecular dynamics in crowded cellular environments
- 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
ハイドロトロープとしてのATP：細胞環境シミュレーションによる物理化学的解明Principal Investigator
- Principal Investigator
  
  優乙石
- Project Period (FY)
  2019 – 2024
- Research Category
  
  Grant-in-Aid for Scientific Research (C)
- Review Section
  
  Basic Section 32010:Fundamental physical chemistry-related
- Research Institution
  Maebashi Institute of Technology
Breakthrough on the high pressure biomolecule reaction with computational chemistry of the volume changePrincipal Investigator
- Principal Investigator
  
  Yu Isseki
- Project Period (FY)
  2013 – 2016
- Research Category
  
  Grant-in-Aid for Scientific Research (C)
- Research Field
  
  Physical chemistry
- Research Institution
  Institute of Physical and Chemical Research
Microscopic breakthrough in the molecular crowding effects promotethe functions of biomoleculesPrincipal Investigator
- Principal Investigator
  
  YU Isseki
- Project Period (FY)
  2010 – 2012
- Research Category
  
  Grant-in-Aid for Young Scientists (B)
- Research Field
  
  Physical chemistry
- Research Institution
  Aoyama Gakuin University
Molecular Informatical Breakthrough on the Water Molecule Network Controlled by Biomacromolecules and CosolventsPrincipal Investigator
- Principal Investigator
  
  YU Isseki
- Project Period (FY)
  2007 – 2009
- Research Category
  
  Grant-in-Aid for Young Scientists (B)
- Research Field
  
  Physical chemistry
- Research Institution
  Aoyama Gakuin University
  Nagoya University

[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] すぐできる分子シミュレーションビギナーズマニュアル2008
- Author(s)
  長岡正隆(編・著)優乙石, 他(著)
- Total Pages
  291
- Publisher
  講談社サイエンティフィク
- Data Source
  KAKENHI-PROJECT-19750004
[Book] すぐできる分子シミュレーションビギナーズマニュアル2008
- Author(s)
  長岡正隆編・著優乙石, 他7名著
- Publisher
  講談社
- Data Source
  KAKENHI-PROJECT-19750004
[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] 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] 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] 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] 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] Structural insights into the complex of oncogenic KRas4BG12V and Rgl2, a RalA/B activator2023
- Author(s)
  M. Tariq, T. Ikeya, N. Togashi, L. Fairall, S. Kamei, S. Mayooramurugan, L.R. Abbott, A. Hasan, C. Bueno-Alejo, S. Sukegawa, B. Romartinez-Alonso, M.A.M. Campillo, A.J. Hudson, Y. Ito, J.W.R. Schwabe, C. Dominguez, K. Tanaka
- Journal Title
  
  Life Sci. Alliance
  
  Volume: 7 Issue: 1 Pages: e202302080-e202302080
- DOI
  10.26508/lsa.202302080
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-21K06114, KAKENHI-PLANNED-19H05773, KAKENHI-PROJECT-19H05645, KAKENHI-PROJECT-21H02419
[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] Interactions of the N- and C-Terminal SH3 Domains of Drosophila Drk with the Proline-Rich Peptides from Sos and Dos2023
- Author(s)
  P.M. Sayeesh, M. Iguchi, Y. Suemoto, J. Inoue, K. Inomata, T. Ikeya, Y. Ito
- Journal Title
  
  Int. J. Mol. Sci.
  
  Volume: 24 Issue: 18 Pages: 14135-14135
- DOI
  10.3390/ijms241814135
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-21K06114, KAKENHI-PLANNED-19H05773, KAKENHI-PROJECT-19H05645, KAKENHI-PROJECT-21H02419
[Journal Article] Direct Observation of Membrane-Associated H-Ras in the Native Cellular Environment by In-Cell <sup>19</sup>F-NMR Spectroscopy2023
- Author(s)
  Ikari Masaomi、Yagi Hiromasa、Kasai Takuma、Inomata Kohsuke、Ito Masahiro、Higuchi Kae、Matsuda Natsuko、Ito Yutaka、Kigawa Takanori
- Journal Title
  
  JACS Au
  
  Volume: 3 Issue: 6 Pages: 1658-1669
- DOI
  10.1021/jacsau.3c00108
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-20K06533, KAKENHI-PLANNED-19H05773, KAKENHI-PROJECT-19H05645, KAKENHI-PROJECT-21H02419
[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] 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] 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] 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] Insight into the C-terminal SH3 domain mediated binding of Drosophila Drk to Sos and Dos2022
- Author(s)
  Sayeesh P.M., Ikeya, T., Sugasawa, H., Watanabe, R., Mishima, M., Inomata, K., & Ito, Y.
- Journal Title
  
  Biochem. Biophys. Res. Commun.
  
  Volume: 625 Pages: 87-93
- DOI
  10.1016/j.bbrc.2022.08.007
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-21K06114, KAKENHI-PROJECT-19H05645, KAKENHI-PROJECT-21H02419, KAKENHI-PLANNED-19H05773
[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] 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] 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] 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] 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] 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] 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] 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] Structural basis of the protochromic green/red photocycle of the chromatic acclimation sensor RcaE2021
- Author(s)
  Takayuki Nagae, Masashi Unno, Taiki Koizumi, Yohei Miyanoiri, Tomotsumi Fujisawa, Kento Masui, Takanari Kamo, Kei Wada, Toshihiko Eki, Yutaka Ito, Yuu Hirose, Masaki Mishima
- Journal Title
  
  Proceedings of the National Academy of Sciences
  
  Volume: 118(20) Issue: 20
- DOI
  10.1073/pnas.2024583118
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-19K06707, KAKENHI-PLANNED-19H05773, KAKENHI-PROJECT-19H03169, KAKENHI-PROJECT-21H02419, KAKENHI-PROJECT-21K04997, KAKENHI-PLANNED-21H05260, KAKENHI-PROJECT-19H05645, KAKENHI-PROJECT-20H03196
[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] Protein-Protein Interactions in Cellular Environments: Theoretical study with Large-scale All-atom Molecular Dynamics Simulations2021
- Author(s)
  優乙石,　杉田治
- Journal Title
  
  Frontier, Journal of the Japan Society of Theoretical Chemistry
  
  Volume: 3 Pages: 2-8
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-19K05389
[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] 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] 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] 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] 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] 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] 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] 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] 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] Domain selective labeling for NMR studies of multidomain proteins by domain ligation using highly active sortase A2020
- Author(s)
  Aizu Takahiro、Suzuki Takumi、Kido Akihiro、Nagai Kan、Kobayashi Ayaho、Sugiura Reiko、Ito Yutaka、Mishima Masaki
- Journal Title
  
  Biochimica et Biophysica Acta (BBA) - General Subjects
  
  Volume: 1864 Issue: 2 Pages: 129419-129419
- DOI
  10.1016/j.bbagen.2019.129419
- Peer Reviewed
- Data Source
  KAKENHI-PLANNED-19H05773, KAKENHI-PROJECT-19H03169, KAKENHI-PROJECT-19H03376, 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] In-cell NMR as a sensitive tool to monitor physiological condition of Escherichia coli2020
- Author(s)
  Sugiki Toshihiko、Yamaguchi Yoshihiro、Fujiwara Toshimichi、Inouye Masayori、Ito Yutaka、Kojima Chojiro
- Journal Title
  
  Scientific Reports
  
  Volume: 10 Issue: 1 Pages: 2466-2466
- DOI
  10.1038/s41598-020-59076-2
- NAID
  120006952208
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PUBLICLY-19H04856, KAKENHI-PLANNED-19H05773, KAKENHI-PROJECT-17H03641, 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] 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] 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] In situ structural biology using in-cell NMR2020
- Author(s)
  Nishida Noritaka、Ito Yutaka、Shimada Ichio
- Journal Title
  
  Biochimica et Biophysica Acta (BBA) - General Subjects
  
  Volume: 1864 Issue: 2 Pages: 129364-129364
- DOI
  10.1016/j.bbagen.2019.05.007
- Peer Reviewed
- Data Source
  KAKENHI-WRAPUP-19H05452, KAKENHI-PLANNED-19H05773, KAKENHI-PROJECT-17H06097, KAKENHI-PROJECT-19H05645
[Journal Article] バクテリア細胞質中の代謝物－蛋白質間相互作用：全原子細胞質モデルと大規模分子動力学計算による理論的研究2017
- Author(s)
  優乙石, 杉田有治
- Journal Title
  
  分子シミュレーション研究会誌「アンサンブル」
  
  Volume: Vol. 19, No. 2 Pages: 75-80
- NAID
  130006729057
- Data Source
  KAKENHI-PROJECT-25410025
[Journal Article] Influence of Protein Crowder Size on Hydration Structure and Dynamics in Macromolecular Crowding2017
- Author(s)
  Po-hung Wang, Isseki Yu, Michael Feig, Yuji Sugita
- Journal Title
  
  Chemical Physics Letters
  
  Volume: 671 Pages: 63-70
- DOI
  10.1016/j.cplett.2017.01.012
- Peer Reviewed / Acknowledgement Compliant / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-25410025
[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] Spatio-Temporal Characteristics of Transfer Free Energy of Apomyoglobin into the Crowding Condition with Trimethylamine N-oxide: A Study with Three Types of the Kirkwood-Buff Integral2012
- Author(s)
  Isseki Yu*, Kyoko Nakada, Masataka Nagaoka
- Journal Title
  
  Journal of Physical Chemistry B
  
  Volume: 116 Pages: 4080-4088
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-22750015
[Journal Article] Spatio-Temporal Characteristics of the Transfer Free Energy of Apomyoglobin into the Molecular Crowding Condition with Trimethylamine N-oxide : A Study with Three Types of the Kirkwood-Buff Integral2012
- Author(s)
  Isseki Yu, Nakada Kyoko, Nagaoka Masataka
- Journal Title
  
  Journal of Physical Chemistry B
  
  Volume: 116 Issue: 13 Pages: 4080-4088
- DOI
  10.1021/jp300380p
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-22750015
[Journal Article] Influence of Hydrostatic Pressure on Dynamics and Spatial Distribution of Protein Partial Molar Volume: Time-Resolved Surficial Kirkwood-Buff Approach2010
- Author(s)
  Isseki Yu*, Masayoshi Takayanagi, Masataka Nagaoka
- Journal Title
  
  Journal of Physical Chemistry B
  
  Volume: 114 Pages: 12392-12397
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-22750015
[Journal Article] Influence of Hydrostatic Pressure on Dynamics and Spatial Distribution of Protein Partial Molar Volume : Time-Resolved Surficial Kirkwood-Buff Approach2010
- Author(s)
  優乙石, 田崎智大, 中田恭子, 長岡正隆
- Journal Title
  
  Journal of Physical Chemistry B
  
  Volume: 114 Pages: 12392-12397
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-22750015
[Journal Article] Energy Flow Analysis in Proteins via Ensemble Molecular Dynamics Simulations: Time-Resolved Vibrational Analysis and Surficial Kirkwood-Buff Theory2009
- Author(s)
  Masataka Nagaoka, Isseki Yu, Masayoshi Takayanagi
- Journal Title
  
  Proteins: Energy, Heat and Signal Flow (D.M. Leitner and I.E. Straub, Eds. )
  
  Pages: 169-196
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-19750004
[Journal Article] Carrier Method for the General Evaluation and Control of Pose, Molecular Conformation, Tracking, and the Like2009
- Author(s)
  Eckhard Hitzer, Kanta Tachibana, Sven Buchholz and Isseki Yu
- Journal Title
  
  Advances in Applied Clifford Algebras (印刷中)
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-19750004
[Journal Article] Energy Flow Analysis in Proteins via Ensemble Molecular Dynamics Simulations : Time-Resolved Vibrational Analysis and Surficial Kirkwood-Buff Theory2009
- Author(s)
  Masataka Nagaoka, Isseki Yu, Masayoshi Takayanagi
- Journal Title
  
  Proteins : Energy, Heat and Signal Flow
  
  Pages: 169-196
- Data Source
  KAKENHI-PROJECT-19750004
[Journal Article] Intrinsic Alterations in the Partial Molar Volume on the Protein Denaturation: Surficial Kirkwood-Buff Approach2009
- Author(s)
  Isseki Yu, Masayoshi Takayanagi, Masataka Nagaoka
- Journal Title
  
  Journal of Physical Chemistry B 113
  
  Pages: 3543-3547
- Data Source
  KAKENHI-PROJECT-19750004
[Journal Article] IntrinSiC Alterations in the Partial Molar Volume on the Protein Denaturation : Surficial Kirkwood-Buff Approach2009
- Author(s)
  Isseki Yu, Masayoshi Takayanagi and Masataka Nagaoka
- Journal Title
  
  Journal of PhySiCal Chemistry B 113
  
  Pages: 3543-3547
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-19750004
[Journal Article] Carrier Method for the General Evaluation and Control of Pose, Molecular Conformation, Tracking, etc.2008
- Author(s)
  Eckhard Hitzer, Kanta Tachibana, Sven Buchholz, Isseki Yu
- Journal Title
  
  Advances in Applied Clifford Algebras 19
  
  Pages: 339-364
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-19750004
[Journal Article] Surficial Kirkwood-Buff Approach on the Preferential Interaction of Urea and Ectoine with Protein2008
- Author(s)
  Isseki Yu, Masataka Nagaoka
- Journal Title
  
  Proceedings of International Symposium on Frontiers of Computational Science
  
  Pages: 9-14
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-19750004
[Journal Article] Microscopic Understanding of Preferential Exclusion of Compatible Solute Ectoine: Direct Interaction and Hydration Alteration2007
- Author(s)
  Isseki Yu, Masataka Nagaoka
- Journal Title
  
  Journal of Physical Chemistry B 111
  
  Pages: 10231-10238
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-19750004
[Journal Article] Microscopic Understanding of Preferential Exclusion of Compatible Solute Ectoine: Direct Interaction and Hydration Alteration.2007
- Author(s)
  優乙石, 長岡正隆
- Journal Title
  
  Journal of Physical Chemistry B 111
  
  Pages: 10231-10238
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-19750004
[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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] In-cell NMR studies of the Keap1-Nrf2 system2023
- Author(s)
  Yutaka Ito，Mei Toyoda，Shiori Suehiro，Kaito Shima，Teppei Ikeya，Takafumi Suzuki, Masayuki Yamamoto, Kohsuke Inomata
- Organizer
  Asia-Pacific Nuclear Magnetic Resonance (APNMR) 2023
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-19H05645
[Presentation] Interaction of N-and C-terminal SH3 domains of Drosophila adapter protein Drk with Sos and Dos2023
- Author(s)
  Sayeesh PM，Mayuki Iguchi，Haruka Sugasawa，Kahsuke Inomata，Teppei Ikeya，Yutaka Ito
- Organizer
  The 19th European Magnetic Resonance Congress
- 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回生物物理学会年会
- Invited
- 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-PROJECT-19H05645
[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] Structural and dynamic studies on the Drosophila adapter Protein Drk2023
- Author(s)
  Sayeesh PM，Mayumi Iguchi，Teppei Ikeya，Yutaka Ito
- Organizer
  第62回NMR討論会
- Data Source
  KAKENHI-PROJECT-19H05645
[Presentation] Theoretical study of the influence of solvent conditions on the structure and interaction of core region in LC domain of FUS2023
- Author(s)
  Suzuka Tokunaga, Isseki Yu
- Organizer
  The 61st Annual Meeting of the Biophysical Society of Japan
- Data Source
  KAKENHI-PROJECT-19K05389
[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-19K05389
[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] 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] 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] NMR studies of a Drosophila adapter protein, Drk2022
- Author(s)
  Sayeesh, PM, Teppei Ikeya, Haruka Sugasawa, Riki Watanabe, Yutaka Ito
- Organizer
  第1回生命金属科学シンポジウム
- 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] Protein behaviours under intracellular crowding environments2022
- Author(s)
  Yutaka Ito
- Organizer
  TMU Workshop on Protein NMR
- Invited
- 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] 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] 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] Solution NMR approaches to 3D structure determination of proteins in living cells2022
- Author(s)
  Yutaka Ito
- Organizer
  The Protein Society Webinar “Exploring Proteins in Living Cells”
- Invited / Int'l Joint Research
- 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] 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-19K05389
[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] Protein structure determination by NMR: conformational multiplicity and the effects of macromolecular crowding2022
- Author(s)
  Yutaka Ito
- Organizer
  The 7th International Symposium on Drug Discovery and Design by NMR
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-19H05645
[Presentation] Solution NMR approaches to 3D structure determination of proteins in living eukaryotic cells2021
- Author(s)
  Yutaka Ito, Kohsuke Inomata, Teppei Ikeya
- Organizer
  22nd International Society of Magnetic Resonance Conference (ISMAR)
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-19H05645
[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] Multi-state structure determination and dynamics analysis reveals a new ubiquitin-recognition mechanism in yeast ubiquitin C-terminal hydrolase2021
- Author(s)
  Teppei Ikeya, Mayu Okada, Yutaka Tateishi, Eri Nojiri, Tsutomu Mikawa, Sundaresan Rajesh, Hiroki Ogasa, Takumi Ueda, Hiromasa Yagi, Toshiyuki Kohno, Takanori Kigawa, Ichio Shimada, Peter Guentert, Yutaka Ito
- Organizer
  22nd International Society of Magnetic Resonance Conference (ISMAR)
- 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] 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] Insight into the C-terminal SH3 mediated binding of Drosophila Drk towards Sos and Dos2021
- Author(s)
  Sayeesh. P. M., Teppei Ikeya, Haruka Sugasawa, Riki Watanabe, Yutaka Ito
- Organizer
  22nd International Society of Magnetic Resonance Conference (ISMAR)
- Int'l Joint Research
- 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-19K05389
[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] 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] Development of Trajectory Analyzer for Cellular-Scale Molecular Dynamics Simulations2021
- Author(s)
  優乙石, 杉田有治
- Organizer
  第59回生物物理学会年会
- Data Source
  KAKENHI-PROJECT-19K05389
[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] 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] 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] 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] 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] Insight into the C-terminal SH3 mediated binding of Drosophila Drk towards Sos and Dos2021
- Author(s)
  Sayeesh. P. M., Teppei Ikeya, Haruka Sugasawa, Riki Watanabe, Yutaka Ito
- Organizer
  第44回日本分子生物学会
- 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] Reduced protein-protein interactions in the cellular crowding with binding of nucleoside triphosphates2020
- Author(s)
  Isseki Yu, Michael Feig, and Yuji Sugita
- Organizer
  第58回生物物理学会年会
- Data Source
  KAKENHI-PROJECT-19K05389
[Presentation] All-atom molecular dynamics simulation of the altered protein-protein interaction with metabolites and ions in the cytoplasm.2020
- Author(s)
  Isseki Yu
- Organizer
  Biophysical Society 64th Annual Meeting
- Int'l Joint Research
- 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] All-atom molecular dynamics simulation of the altered protein-protein interaction with metabolites and ions in the cytoplasm2020
- Author(s)
  Isseki Yu, Michael Feig, and Yuji Sugita
- Organizer
  Biophysical Society 64th Annual Meeting
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-19K05389
[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] 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] 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] 細胞質中の代謝物によって改変される蛋白質間相互作用の全原子分子動力学シミュレーション2019
- Author(s)
  優　乙石
- Organizer
  第33回分子シミュレーション討論会
- 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] Solution NMR approaches to 3D structure determination of proteins in living eukaryotic cells2019
- Author(s)
  Yutaka Ito, Teppei Ikeya
- Organizer
  The 42th Annual Meeting of the Molecular Biology Society of Japan
- 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] High-resolution protein 3D structure determination in living eukaryotic cells2019
- Author(s)
  Takashi Tanaka, Yutaka Ito, et al.
- Organizer
  The 12th Australian and New Zealand Society for Magnetic Resonance Conference (ANZMAG conference 2019)
- 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] 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] 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] 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] All-atom molecular dynamics simulation of the reduced protein-protein interaction with metabolites in the cytoplasm2019
- Author(s)
  Isseki Yu, Michael Feig, and Yuji Sugita
- Organizer
  第57回生物物理学会年会
- Data Source
  KAKENHI-PROJECT-19K05389
[Presentation] All-atom molecular dynamics simulation of the reduced protein-protein interaction with metabolites in the cytoplasm.2019
- Author(s)
  Isseki Yu
- Organizer
  第57回日本生物物理学会年会
- 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] 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] 細胞質中の代謝物によって改変される蛋白質間相互作用の全原子分子動力学シミュレーション2019
- Author(s)
  優乙石, Feig Michael, 杉田有治
- Organizer
  第33 回分子シミュレーション討論会
- Data Source
  KAKENHI-PROJECT-19K05389
[Presentation] Solution NMR approaches to 3D structure determination of proteins in living eukaryotic cells2019
- Author(s)
  Yutaka Ito, Teppei Ikeya
- Organizer
  33rd Annual Symposium of the Protein Society, USA
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-19H05645
[Presentation] High resolution protein 3D structure determination in living eukaryotic cells2019
- Author(s)
  Teppei Ikeya, Yutaka Ito
- Organizer
  The 8th Asia Pacific NMR Symposium, Singapore
- Invited / Int'l Joint Research
- 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] 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] Multi-state protein structure determination by integrated analysis of several NMR data sets2019
- Author(s)
  Teppei Ikeya, Yutaka Ito
- Organizer
  IPR seminar
- 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] 全原子細胞質モデルと大規模分子動力学計算による細胞内生体分子ダイナミクスの理論的解明2017
- Author(s)
  優乙石
- Organizer
  物性研究所スパコン共同利用・CCMS合同研究会「計算物質科学の今と未来」
- Place of Presentation
  東京大学　千葉県柏市
- Year and Date
  2017-04-04
- Invited
- Data Source
  KAKENHI-PROJECT-25410025
[Presentation] Theoretical Study of the Influence of Cellular Crowding on the Dynamics and Interactions of proteins2016
- Author(s)
  優乙石、森貴治、安藤格士、Jaewoon Jung、原田隆平、Michael Feig、杉田有治
- Organizer
  第39回日本分子生物学会年会
- Place of Presentation
  パシフィコ横浜神奈川県横浜市
- Year and Date
  2016-12-01
- Invited
- Data Source
  KAKENHI-PROJECT-25410025
[Presentation] Influence of Macromolecular Crowding on the Dynamics and Interactions of proteins: All-atom Molecular Dynamics Study2016
- Author(s)
  Isseki Yu, Takaharu Mori, Tadashi Ando, Ryuhei Harada, Jaewoon Jung, Michael Feig, Yuji Sugita
- Organizer
  第54回日本生物物理学会年会
- Place of Presentation
  エポカルつくば　茨城県つくば市
- Year and Date
  2016-11-26
- Data Source
  KAKENHI-PROJECT-25410025
[Presentation] バクテリア細胞質中の混み合い環境下における蛋白質と代謝物の全原子分子動力学シミュレーション2015
- Author(s)
  Isseki Yu, Takaharu Mori, Jaewoon Jung, Tadashi Ando, Ryuhei Harada, Michael Feig, Yuji Sugita
- Organizer
  38回日本分子生物学会年会、88回　日本生化学大会　合同大会
- Place of Presentation
  兵庫県・神戸市
- Year and Date
  2015-12-01
- Data Source
  KAKENHI-PROJECT-25410025
[Presentation] Dynamics, Stability, and Interactions of Proteins and Metabolites in Bacterial Cytoplasm: All-atom Molecular Dynamics Study2015
- Author(s)
  Isseki Yu, Takaharu Mori, Jaewoon Jung, Tadashi Ando, Ryuhei Harada, Michael Feig, Yuji Sugita
- Organizer
  第53回日本生物物理学会年会
- Place of Presentation
  石川県・金沢大学
- Year and Date
  2015-09-15
- Invited
- Data Source
  KAKENHI-PROJECT-25410025
[Presentation] Atomistic Molecular Dynamics Simulation of a Complete Model of Bacterial Cytoplasm2015
- Author(s)
  Isseki Yu, Takaharu Mori, Jaewoon Jung, Tadashi Ando, Ryuhei Harada, Michael Feig, Yuji Sugita
- Organizer
  International Conference on Computational Methods (ICCM) 2015
- Place of Presentation
  ニュージーランド・オークランド
- Year and Date
  2015-07-15
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-25410025
[Presentation] 細胞内環境での蛋白質の分子運動と機能2015
- Author(s)
  Isseki Yu, Takaharu Mori, Jaewoon Jung, Tadashi Ando, Ryuhei Harada, Michael Feig, Yuji Sugita
- Organizer
  生命医薬情報学連合大会2015大会スポンサーセッション生命科学におけるインフォマティクスと物理化学の融合
- Place of Presentation
  京都・京都大学・宇治キャンパス
- Year and Date
  2015-10-30
- Invited
- Data Source
  KAKENHI-PROJECT-25410025
[Presentation] Dynamics and Interactions of Macromolecules in the Cytoplasm of Mycoplasma Genitalium: All-atom Molecular Dynamics Study2014
- Author(s)
  Isseki Yu, Takaharu Mori, Jaewoon Jung, Tadashi Ando, Ryuhei Harada, Michael Feig, Yuji Sugita
- Organizer
  Workshop on Computer Modeling and Simulation of Biomolecular Systems
- Place of Presentation
  理化学研究所/和光市/埼玉県
- Year and Date
  2014-09-22
- Data Source
  KAKENHI-PROJECT-25410025
[Presentation] Space-Time Characteristics of the Protein Thermodynamic Quantities under the Molecular Crowding Condition of Cytoplasm in Extremophiles: Kirkwood-Buff Approach Combined with Molecular Dynamics Simulation2014
- Author(s)
  Isseki Yu
- Organizer
  Biophysical Society 58th Annual Meeting
- Place of Presentation
  サンフランシスコ
- Data Source
  KAKENHI-PROJECT-25410025
[Presentation] Kirkwood-Buff積分法による蛋白質移相自由エネルギーの三次元可視化:　細胞内分子混雑効果の微視的理解に向けて2013
- Author(s)
  優　乙石
- Organizer
  計算統計物理学第4回研究会
- Place of Presentation
  山口大学
- Invited
- Data Source
  KAKENHI-PROJECT-25410025
[Presentation] 蛋白質移相自由エネルギーの空間分布に与える溶質表面特性の影響:オスモライトによる分子クラウディング環境下の場合2012
- Author(s)
  優乙石、中田恭子、長岡正隆
- Organizer
  第6回分子科学討論会
- Place of Presentation
  東京大学
- Data Source
  KAKENHI-PROJECT-22750015
[Presentation] 蛋白質移相自由エネルギーの空間分布に与える溶質表面特性の影響：オスモライトによる分子クラウディング環境下の場合2012
- Author(s)
  優　乙石
- Organizer
  第6回分子科学討論会東京大学
- Place of Presentation
  東京大学
- Data Source
  KAKENHI-PROJECT-22750015
[Presentation] TMAO 添加による蛋白質溶媒和自由エネルギー変化の微視的解明: 3 次元カークウッド-バフ積分法によるマッピング解析2012
- Author(s)
  優乙石、中田恭子、長岡正隆
- Organizer
  第26回分子シミュレーション討論会
- Place of Presentation
  九州大学
- Data Source
  KAKENHI-PROJECT-22750015
[Presentation] カークウッド‐バフ積分法による蛋白質移相自由エネルギーの計算と映像化: 分子クラウディング環境の微視的理解に向けて2012
- Author(s)
  優乙石、中田恭子、長岡正隆
- Organizer
  第15回理論化学討論会
- Place of Presentation
  仙台市福祉プラザ
- Data Source
  KAKENHI-PROJECT-22750015
[Presentation] トリメチルアミンN-オキシドで模倣した細胞質環境へのアポミオグロビン移相自由エネルギー:カークウッド-バフ積分法による時空間解析2012
- Author(s)
  優乙石、中田恭子、長岡正隆
- Organizer
  日本化学会第92春季年会
- Place of Presentation
  慶応大学
- Year and Date
  2012-03-27
- Data Source
  KAKENHI-PROJECT-22750015
[Presentation] Three-dimensional Imaging of the Protein Transfer Free Energy into the Molecular Crowding Condition with TMAO2012
- Author(s)
  優　乙石
- Organizer
  第50回生物物理学会年会名古屋市　名古屋大学
- Place of Presentation
  名古屋大学
- Data Source
  KAKENHI-PROJECT-22750015
[Presentation] トリメチルアミン N-オキシドで模倣した細胞質環境へのアポミオグロビン移相自由エネルギー:カークウッド‐バフ積分法による時空間解析2012
- Author(s)
  優乙石、中田恭子、長岡正隆
- Organizer
  日本化学会第92 春季年会
- Place of Presentation
  慶応大学
- Year and Date
  2012-03-27
- Data Source
  KAKENHI-PROJECT-22750015
[Presentation] Three-dimensional Imaging of the Protein Transfer Free Energy into the Molecular Crowding Condition with TMAO2012
- Author(s)
  優乙石、中田恭子、長岡正隆
- Organizer
  第50回生物物理学会年会
- Place of Presentation
  名古屋大学
- Data Source
  KAKENHI-PROJECT-22750015
[Presentation] TMAO添加による蛋白質溶媒和自由エネルギー変化の微視的解明： 3次元カークウッド－バフ積分法によるマッピング解析2012
- Author(s)
  優　乙石
- Organizer
  第２６回分子シミュレーション討論会
- Place of Presentation
  九州大学
- Data Source
  KAKENHI-PROJECT-22750015
[Presentation] High Pressure-Induced Hydration Volume Change around the Protein : Kirkwood-Buff Approach combined with Molecular Dynamics Simulation2011
- Author(s)
  優乙石、中田恭子、長岡正隆
- Organizer
  第49回生物物理学会年会
- Place of Presentation
  兵庫県立大学
- Year and Date
  2011-09-17
- Data Source
  KAKENHI-PROJECT-22750015
[Presentation] 高静水圧が及ぼすアポミオグロビンの遠位水和体積変化:分子動力学法と連携するカークウッド‐バフ積分法による考察2011
- Author(s)
  優乙石、中田恭子、長岡正隆
- Organizer
  分子科学討論会 2011
- Place of Presentation
  札幌市札幌コンベンションセンター
- Year and Date
  2011-09-21
- Data Source
  KAKENHI-PROJECT-22750015
[Presentation] High Pressure-Induced Hydration Volume Change around the Protein:Kirkwood-Buff Approach combined with Molecular Dynamics Simulation2011
- Author(s)
  優乙石、中田恭子、長岡正隆
- Organizer
  第49回生物物理学会年会
- Place of Presentation
  兵庫県立大学
- Year and Date
  2011-09-17
- Data Source
  KAKENHI-PROJECT-22750015
[Presentation] 高静水圧が及ぼすアポミオグロビンの遠位水和体積変化:分子動力学法と連携するカークウッド-バフ積分法による考察2011
- Author(s)
  優乙石、中田恭子、長岡正隆
- Organizer
  分子科学討論会2011
- Place of Presentation
  札幌市札幌コンベンションセンター
- Year and Date
  2011-09-21
- Data Source
  KAKENHI-PROJECT-22750015
[Presentation] Molecular Dynamics Picture of Protein Partial Molar Volume Reduction under High Hydrostatic Pressure:Time-Resolved Kirkwood-Buff Approach2010
- Author(s)
  優乙石、中田恭子、長岡正隆
- Organizer
  生物物理学会48回年会
- Place of Presentation
  東北大学
- Year and Date
  2010-09-21
- Data Source
  KAKENHI-PROJECT-22750015
[Presentation] Molecular Dynamics Picture of Protein Partial Molar Volume Reduction under High Hydrostatic Pressure : Time-Resolved Kirkwood-Buff Approach2010
- Author(s)
  優乙石、中田恭子、長岡正隆
- Organizer
  生物物理学会48回年会
- Place of Presentation
  東北大学
- Year and Date
  2010-09-21
- Data Source
  KAKENHI-PROJECT-22750015
[Presentation] アポミオグロビン部分モル体積のダイナミクスおよび空間分布に及ぼす高静水圧の影響:時間分解カークウッド-バフ積分法による考察2010
- Author(s)
  優乙石、中田恭子、長岡正隆
- Organizer
  分子科学討論会2010
- Place of Presentation
  大阪大学
- Year and Date
  2010-09-14
- Data Source
  KAKENHI-PROJECT-22750015
[Presentation] アポミオグロビン部分モル体積のダイナミクスおよび空間分布に及ぼす高静水圧の影響:時間分解カークウッド-バフ積分法による考察2010
- Author(s)
  優乙石、中田恭子、長岡正隆
- Organizer
  分子科学討論会 2010
- Place of Presentation
  大阪大学
- Year and Date
  2010-09-14
- Data Source
  KAKENHI-PROJECT-22750015
[Presentation] 補償溶質エクトインによる蛋白質構造安定化の分子機構:分子動力学シミュレーション法による微視的理解2010
- Author(s)
  優乙石、中田恭子、長岡正隆
- Organizer
  11回極限環境生物学会年会
- Place of Presentation
  京都大学
- Year and Date
  2010-11-15
- Data Source
  KAKENHI-PROJECT-22750015
[Presentation] Solvent Effect on the Protein Structure : Surficial Kirkwood?Buff Approach2009
- Author(s)
  Isseki Yu, Masataka Nagaoka
- Organizer
  International Symposium on Frontiers of Computational Science
- Place of Presentation
  Nagoya, Japan
- Year and Date
  2009-03-16
- Data Source
  KAKENHI-PROJECT-19750004
[Presentation] Protein Volume Paradox and its Molecular Picture : A Study by Surficial Kirkwood-Buff Integral Method2009
- Author(s)
  優乙石, 長岡正隆
- Organizer
  第47回生物物理学会
- Place of Presentation
  徳島
- Year and Date
  2009-10-31
- Data Source
  KAKENHI-PROJECT-19750004
[Presentation] 部分モル体積の空間分布から見たタンパク質変性:カークウツド-パフ積分法による考察2009
- Author(s)
  優乙石、長岡正隆
- Organizer
  第3回分子科学討論会
- Place of Presentation
  名古屋
- Year and Date
  2009-09-22
- Data Source
  KAKENHI-PROJECT-19750004
[Presentation] 表面カークウツド. パフ積分法によるタンパク質部分モル体積不変性の微視的理解2009
- Author(s)
  優乙石、長岡正隆
- Organizer
  理論化学討論会
- Place of Presentation
  東京
- Year and Date
  2009-05-30
- Data Source
  KAKENHI-PROJECT-19750004
[Presentation] Protein Volume Paradox and its Molecular Picture: A Study by Surficial Kirkwood-Buff Integral Method2009
- Author(s)
  優乙石長岡正隆
- Organizer
  第47回生物物理学会年会
- Place of Presentation
  徳島
- Year and Date
  2009-11-01
- Data Source
  KAKENHI-PROJECT-19750004
[Presentation] 表面カークウッド-バフ積分法によるタンパク質部分モル体積不変性の微視的理解2009
- Author(s)
  優乙石, 長岡正隆
- Organizer
  第12回理論化学討論会
- Place of Presentation
  東京
- Year and Date
  2009-05-28
- Data Source
  KAKENHI-PROJECT-19750004
[Presentation] 部分モル体積の空間分布から見たタンパク質変性:カークウッド-パフ積分法による考察2009
- Author(s)
  優乙石, 長岡正隆
- Organizer
  第3回分子科学討論会
- Place of Presentation
  名古屋
- Year and Date
  2009-05-28
- Data Source
  KAKENHI-PROJECT-19750004
[Presentation] Molecular Picture of Protein Volume Paradox : A Studv by Surficial Kirkwood-Buff Integral Method2009
- Author(s)
  優乙石, 長岡正隆
- Organizer
  The fourth Asian Pacific Conference on Theoretical & Computational Chemistry
- Place of Presentation
  ポートディクソンマレーシア
- Year and Date
  2009-12-22
- Data Source
  KAKENHI-PROJECT-19750004
[Presentation] Molecular Picture of Protein Volume Paradox: A Study by Surficial Kirkwood-Buff Integral Method2009
- Author(s)
  Isseki YU, Masataka Nagaoka
- Organizer
  The fourth Asian Pacific Conference on Theoretical & Computational Chemistry
- Place of Presentation
  クアラルンプール
- Year and Date
  2009-12-22
- Data Source
  KAKENHI-PROJECT-19750004
[Presentation] 表面Kirkwood-Buff法による補償溶質エクトイン選択的排除の分子論的理解2008
- Author(s)
  優乙石、長岡正隆
- Organizer
  日本化学会第88回春季会
- Place of Presentation
  東京
- Year and Date
  2008-03-28
- Data Source
  KAKENHI-PROJECT-19750004
[Presentation] Surficial Kirkwood-Buff Approach on the Preferential Interaction of Urea and Ectoine with Protein2008
- Author(s)
  Isseki YU, Masataka Nagaoka
- Organizer
  Intemational Symposium on Frontiers of Computational Science
- Place of Presentation
  名古屋
- Year and Date
  2008-11-29
- Data Source
  KAKENHI-PROJECT-19750004
[Presentation] Surficial Kirkwood?Buff Approach Combined with All-Atom Molecular Dynamics Simulation : Analysis of Solvent Structure around Biomolecules2008
- Author(s)
  Isseki Yu, Masataka Nagaoka
- Organizer
  International Symposium on Frontiers of Computational Science
- Place of Presentation
  Nagoya, Japan
- Year and Date
  2008-11-28
- Data Source
  KAKENHI-PROJECT-19750004
[Presentation] 表面Kirkwood-Buff法による補償溶質エクトイン選択的排除の分子論的理解2008
- Author(s)
  優乙石, 長岡正隆
- Organizer
  日本化学会第88春季年会
- Place of Presentation
  東京
- Year and Date
  2008-03-28
- Data Source
  KAKENHI-PROJECT-19750004
[Presentation] エクトイン水溶液中のタンパク質表面における選択的水和発現機構の分子論的考察2007
- Author(s)
  優乙石, 長岡正隆
- Organizer
  第10同理論化学討論会
- Place of Presentation
  名古屋
- Year and Date
  2007-05-14
- Data Source
  KAKENHI-PROJECT-19750004
[Presentation] エクトイン水溶液中のタンパク質表面における選択的水和発現機構の分子論的考察2007
- Author(s)
  優乙石、長岡正隆
- Organizer
  第10回理論化学討論会
- Place of Presentation
  名古屋
- Year and Date
  2007-05-15
- Data Source
  KAKENHI-PROJECT-19750004
[Presentation] Molecular Mechanism of the Preferential Exclusion of Compatible Solute Ectoine on the Protein Surface2007
- Author(s)
  優乙石, 長岡正隆
- Organizer
  日本生物物理学会第45回年会
- Place of Presentation
  横浜
- Year and Date
  2007-12-23
- Data Source
  KAKENHI-PROJECT-19750004
[Presentation] エクトイン水溶液中のタンパク質および小ペプチド表面における選択的水和の微視的描像2007
- Author(s)
  優乙石, 長岡正隆
- Organizer
  第1回分子科学討論会
- Place of Presentation
  仙台
- Year and Date
  2007-09-20
- Data Source
  KAKENHI-PROJECT-19750004
[Presentation] Molecular Mechanism of the Preferential Exclusion of Compatible Solute Ectoine on the Protein Surface2007
- Author(s)
  優乙石、長岡正隆
- Organizer
  第45回生物物理学会年会
- Place of Presentation
  東京
- Year and Date
  2007-12-23
- Data Source
  KAKENHI-PROJECT-19750004
[Presentation] エクトイン水溶液中のタンパク質および小ペプチド表面における選択的水和2007
- Author(s)
  優乙石、長岡正隆
- Organizer
  第1回分子科学討論会
- Place of Presentation
  仙台
- Year and Date
  2007-09-19
- Data Source
  KAKENHI-PROJECT-19750004
[Presentation] Microscopic Understanding of Preferential Exclusion of Compatible Solute Ectoine: Surficial Kirkwood-Buff Approach2007
- Author(s)
  優乙石, 長岡正隆
- Organizer
  The 3rd Asian Pacific Conference of Theoretical and Computational Chemistry (APCTCIII)
- Place of Presentation
  北京
- Year and Date
  2007-09-23
- Data Source
  KAKENHI-PROJECT-19750004
[Presentation] Microscopic Understanding of Preferential Exclusion of Compatible Solute Ectoine: Surficial Kirkwood-Buff Approach2007
- Author(s)
  Isseki YU, Masataka Nagaoka
- Organizer
  The 3rd Asian Pacific Conference on Theoretical & Computational Chemistry
- Place of Presentation
  北京
- Year and Date
  2007-09-23
- Data Source
  KAKENHI-PROJECT-19750004
[Presentation] Dynamics and Interactions of Macromolecules in the Bacterial Cytoplasm: All-atom Molecular Dynamics Study
- Author(s)
  Isseki Yu, Takaharu Mori, Jaewoon Jung, Tadashi Ando, Ryuhei Harada, Michael Feig, Yuji Sugita
- Organizer
  日本生物物理学会第52回年会
- Place of Presentation
  札幌コンベンションセンター/札幌/北海道
- Year and Date
  2014-09-25 – 2014-09-27
- Data Source
  KAKENHI-PROJECT-25410025
[Presentation] All-atom Molecular Dynamics Simulation of the Complete Model of Bacterial Cytoplasm”
- Author(s)
  Isseki Yu, Takaharu Mori, Jaewoon Jung, Tadashi Ando, Ryuhei Harada, Michael Feig, Yuji Sugita
- Organizer
  第5回AICS国際シンポジウム
- Place of Presentation
  計算科学研究機構/神戸市/兵庫県
- Year and Date
  2014-12-08 – 2014-12-09
- Data Source
  KAKENHI-PROJECT-25410025
[Presentation] The solvent-accessible surface area of proteins affects water structure and dynamics
- Author(s)
  Po-hung Wang, Isseki Yu, Michael Feig, and Yuji Sugita
- Organizer
  日本生物物理学会第52回年会
- Place of Presentation
  札幌コンベンションセンター/札幌/北海道
- Year and Date
  2014-09-25 – 2014-09-27
- Data Source
  KAKENHI-PROJECT-25410025

1. Sugita Yuji (80311190)

# of Collaborated Projects: 2 results

# of Collaborated Products: 95 results
2. 伊藤隆 (80261147)

# of Collaborated Projects: 1 results

# of Collaborated Products: 23 results
3. Wang Po-hung

# of Collaborated Projects: 1 results

# of Collaborated Products: 2 results
4. HIROSE Yu

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results
5. IKEYA Teppei

# of Collaborated Projects: 0 results

# of Collaborated Products: 3 results
6. TAKITA Ryo

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results
7. NISHIDA Noritaka

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results
8. 松永康佑

# of Collaborated Projects: 0 results

# of Collaborated Products: 2 results
9. 李秀栄

# of Collaborated Projects: 0 results

# of Collaborated Products: 3 results
10. 笠原健人

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results
11. 鄭載運

# of Collaborated Projects: 0 results

# of Collaborated Products: 2 results
12. 森貴治

# of Collaborated Projects: 0 results

# of Collaborated Products: 5 results
13. 児嶋長次郎

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results
14. 八木清

# of Collaborated Projects: 0 results

# of Collaborated Products: 2 results
15. 葛西卓磨

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results

Yu Isseki 優 乙石

優 乙石 ユウ イッセキ

YU Isseki 優 乙石

Research Projects

Research Products

Co-Researchers

Multi-scale molecular dynamics simulation on biomolecular dynamics in crowded cellular environments

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ハイドロトロープとしてのATP：細胞環境シミュレーションによる物理化学的解明Principal Investigator

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Breakthrough on the high pressure biomolecule reaction with computational chemistry of the volume changePrincipal Investigator

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Microscopic breakthrough in the molecular crowding effects promotethe functions of biomoleculesPrincipal Investigator

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Molecular Informatical Breakthrough on the Water Molecule Network Controlled by Biomacromolecules and CosolventsPrincipal Investigator

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[Book] In-cell NMR Spectroscopy: From Molecular Sciences to Cell Biology2019

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[Book] Biomolecular Simulation: Methods and Protocols2019

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[Book] すぐできる分子シミュレーションビギナーズマニュアル2008

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[Book] すぐできる分子シミュレーションビギナーズマニュアル2008

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[Journal Article] SPANA: Spatial decomposition analysis for cellular-scale molecular dynamics simulations2024

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[Journal Article] Free-energy landscapes of transmembrane homodimers by bias-exchange adaptively biased molecular dynamics2024

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[Journal Article] GENESIS CGDYN: large-scale coarse-grained MD simulation with dynamic load balancing for heterogeneous biomolecular systems2024

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[Journal Article] Allosteric regulation of ホイ-reaction stage I in tryptophan synthase upon the ホア-ligand binding2023

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[Journal Article] Development of Hidden Markov Modeling of Molecular Orientations and Structures from High-Speed Atomic Force Microscopy Time-Series Images2023

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Yu Isseki 優乙石

優乙石ユウイッセキ

YU Isseki 優乙石