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Development of Molecular Dynamics Classification Theories for Life Science and Drug Design

Research Project

Project/Area Number 15KT0103
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section特設分野
Research Field Mathematical Sciences in Search of New Cooperation
Research InstitutionThe University of Tokyo

Principal Investigator

Yamashita Takefumi  東京大学, 先端科学技術研究センター, 特任准教授 (50615622)

Co-Investigator(Kenkyū-buntansha) 児玉 大樹  東京大学, 大学院数理科学研究科, 特任准教授 (40466826)
Project Period (FY) 2015-07-10 – 2020-03-31
Project Status Completed (Fiscal Year 2019)
Budget Amount *help
¥4,680,000 (Direct Cost: ¥3,600,000、Indirect Cost: ¥1,080,000)
Fiscal Year 2018: ¥910,000 (Direct Cost: ¥700,000、Indirect Cost: ¥210,000)
Fiscal Year 2017: ¥910,000 (Direct Cost: ¥700,000、Indirect Cost: ¥210,000)
Fiscal Year 2016: ¥910,000 (Direct Cost: ¥700,000、Indirect Cost: ¥210,000)
Fiscal Year 2015: ¥1,950,000 (Direct Cost: ¥1,500,000、Indirect Cost: ¥450,000)
Keywords分子動力学シミュレーション / 分子生物学 / 数理科学 / 計算幾何学 / 時系列解析 / 分子シミュレーション / ダイナミクス変化 / 分子動力学 / タンパク質 / 分子ダイナミクス / 生体分子 / 分子設計 / エントロピー / 計算幾何 / 構造解析 / タンパク質-リガンド相互作用 / 解析理論
Outline of Final Research Achievements

Recently, advances in computer power have enabled large-scale molecular dynamics simulations of biomolecules. In this study, we introduced several methods to extract various dynamics features from molecular dynamics simulations based on mathematical techniques. For example, we showed that the skeletal core enabled us to remove the effect of apparent motion in the analysis. In addition, we demonstrated that the singular spectrum transformation could detect the motion mode change easily and automatically.

Academic Significance and Societal Importance of the Research Achievements

本研究は、最近の発展が目覚ましい分子動力学シミュレーションと数理科学的解析との融合を狙ったものである。実際に、skeletal coreや特異スペクトル変換の技術はこれまで検知できなかった生体分子の特徴を取り出すことに成功している。数理科学的手法で新たに解析できるようになった生体分子の特徴は、今後、生体分子の機能を解析したり医薬品を設計したりする基盤として役立つと考えられる。

Report

(6 results)
  • 2019 Annual Research Report   Final Research Report ( PDF )
  • 2018 Research-status Report
  • 2017 Research-status Report
  • 2016 Research-status Report
  • 2015 Research-status Report
  • Research Products

    (43 results)

All 2020 2019 2018 2017 2016 Other

All Journal Article (14 results) (of which Peer Reviewed: 11 results,  Open Access: 10 results,  Acknowledgement Compliant: 2 results) Presentation (26 results) (of which Int'l Joint Research: 14 results,  Invited: 18 results) Remarks (3 results)

  • [Journal Article] Modified AMBER force-field (FUJI) parameters for sulfated and phosphorylated tyrosine residues: Development and application to CCR5-derived peptide systems2019

    • Author(s)
      Yamashita Takefumi, Okajima Ryo, Miyanabe Kazuhiro, Tsumoto Kouhei
    • Journal Title

      AIP Conf. Proc.

      Volume: 2186 Pages: 030013-030013

    • DOI

      10.1063/1.5137924

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Versatility of RNA-Binding Proteins in Living Cells2019

    • Author(s)
      R. Kurokawa et al.
    • Journal Title

      Biomedical Sciences

      Volume: 5 Issue: 1 Pages: 7-13

    • DOI

      10.11648/j.bs.20190501.12

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] A SNP in a Steroidogenic Enzyme Is Associated with Phenotypic Sex in Seriola Fishes2019

    • Author(s)
      T. Koyama, M. Nakamoto#, K. Morishima#, R. Yamashita#, T. Yamashita#, K. Sasaki, Y. Kuruma, N. Mizuno, M. Suzuki, K. Okada, R. Ieda, T. Uchino, S. Tasumi, S. Hosoya, S. Uno, J. Koyama, A. Toyoda, K. Kikuchi, T. Sakamoto
    • Journal Title

      Current Biology

      Volume: 29 Issue: 11 Pages: 1901-1909

    • DOI

      10.1016/j.cub.2019.04.069

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] 構造生物学2.0としての分子動力学シミュレーション:創薬応用への道2019

    • Author(s)
      山下雄史
    • Journal Title

      月刊「細胞」(The Cell)

      Volume: 51 Pages: 606-607

    • Related Report
      2019 Annual Research Report
  • [Journal Article] 抗体医薬品設計に IT 革命を: 理論と計算による挑戦2019

    • Author(s)
      山下雄史
    • Journal Title

      月刊「細胞」(The Cell)

      Volume: 51 Pages: 344-347

    • Related Report
      2019 Annual Research Report
  • [Journal Article] Efficiency Strategy for Peptide Design: a Comparative Study on All-atom, Coarse-grained, and Machine Learning Approaches2018

    • Author(s)
      T. Yamashita, R. Okajima, and N. Shoji
    • Journal Title

      AIP Conf. Proc.

      Volume: 2040 Pages: 020014-020014

    • DOI

      10.1063/1.5079056

    • Related Report
      2018 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Liquid Structures Characterized by a Combination of the Persistent Homology Analysis and Molecular Dynamics Simulation2018

    • Author(s)
      K. Sasaki, R. Okajima, and T. Yamashita
    • Journal Title

      AIP Conf. Proc.

      Volume: 2040 Pages: 020014-020014

    • DOI

      10.1063/1.5079057

    • Related Report
      2018 Research-status Report
    • Open Access
  • [Journal Article] Multiplicity in Long Noncoding RNA Biomedical Sciences2018

    • Author(s)
      3.R. Kurokawa, R. Komiya, T. Oyoshi, Y. Matsuno, H. Tani, M. Katahira, K. Hitachi, Y. Iwashita, T. Yamashita, K. Kondo, R. Yoneda, Y. Yamaoki, N. Ueda, T. Mashima, N. Kobayashi, T. Nagata, A. Kiyoishi, M. Miyake, F. Kano, M. Murata1, N. Hamad, K. Sasaki, N. Shoji
    • Journal Title

      Biomedical Sciences

      Volume: 4 Issue: 2 Pages: 18-23

    • DOI

      10.11648/j.bs.20180402.11

    • Related Report
      2018 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Tyrosine sulfation restricts the conformational ensemble of a flexible peptide, strengthening the binding affinity for an antibody2018

    • Author(s)
      K. Miyanabe, T. Yamashita, Y. Abe, H. Akiba, Y. Takamatsu, M. Nakakido, T. Hamakubo, T. Ueda, JMM. Caaveiro, and K. Tsumoto
    • Journal Title

      Biochemistry

      Volume: 57 Issue: 28 Pages: 4177-4185

    • DOI

      10.1021/acs.biochem.8b00592

    • Related Report
      2018 Research-status Report
    • Peer Reviewed
  • [Journal Article] Toward rational antibody design: recent advancements in molecular dynamics simulations2018

    • Author(s)
      T. Yamashita
    • Journal Title

      Int. Immunol.

      Volume: 30 Issue: 4 Pages: 133-140

    • DOI

      10.1093/intimm/dxx077

    • Related Report
      2018 Research-status Report 2017 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] An ensemble docking calculation of lysozyme and HyHEL-10: Insight into the binding mechanism2017

    • Author(s)
      Yamashita Takefumi、Takamatsu Yuichiro
    • Journal Title

      AIP Conf. Proc.

      Volume: 1906 Pages: 030022-030022

    • DOI

      10.1063/1.5012301

    • Related Report
      2017 Research-status Report
    • Peer Reviewed
  • [Journal Article] Molecular dynamics analysis to evaluate docking pose prediction2016

    • Author(s)
      Takako Sakano, Md. Iqbal Mahmood, Takefumi Yamashita*, and Hideaki Fujitani
    • Journal Title

      Biophysics and Physicobiology

      Volume: 13 Issue: 0 Pages: 181-194

    • DOI

      10.2142/biophysico.13.0_181

    • NAID

      130005165376

    • ISSN
      2189-4779
    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Towards Physical Understanding of Molecular Recognition in the Cell: Recent Evolution of Molecular Dynamics Techniques and Free Energy Theories2016

    • Author(s)
      T. Yamashita
    • Journal Title

      Biomedical Sciences

      Volume: 2 Pages: 34-47

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] On the Accurate Molecular Dynamics Analysis of Biological Molecules2016

    • Author(s)
      T. Yamashita
    • Journal Title

      AIP Conf. Proc.

      Volume: 1790 Pages: 020026-020026

    • DOI

      10.1063/1.4968652

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Presentation] 分子動力学シミュレーションを用いた抗体設計の可能性: ”動き”に含まれる親和性のエッセンス2020

    • Author(s)
      山下雄史
    • Organizer
      CBI学会講演会「実験と計算化学を用いた抗体医薬設計の最近の進展」
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] Effects of alanine substitution on antigen-antibody interaction: A molecular dynamics study2019

    • Author(s)
      Takefumi Yamashita
    • Organizer
      International Congress on Pure & Applied Chemistry (ICPAC) Yangon 2019
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Effect of the interfacial water molecule on the antigen-antibody interaction: A molecular dynamics study2019

    • Author(s)
      Takefumi Yamashita
    • Organizer
      15th International Conference of Computational Methods in Sciences and Engineering (CC symposium of ICCMSE 2019)
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Mechanism of antibody-affinity enhancement through alanine-substitution2019

    • Author(s)
      山下雄史
    • Organizer
      日本生物物理学会年会(Symposium “New horizon of in-silico drug discovery toward launching post-K computer”)
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] 分子動力学シミュレーションでせまるタンパク質間相互作用2019

    • Author(s)
      山下雄史
    • Organizer
      シンポジウム「化学反応経路探索のニューフロンティア2019」
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] Effect of interface structure on the binding affinity of proteins: A molecular dynamics study2018

    • Author(s)
      Takefumi Yamashita
    • Organizer
      IMS symposium "Water at interfaces 2018"
    • Related Report
      2018 Research-status Report
    • Int'l Joint Research
  • [Presentation] Molecular dynamics in the antibody-antigen recognition2018

    • Author(s)
      Takefumi Yamashita
    • Organizer
      Symposium on Eukaryotic Regulatory Biology in honor of M. Geoffrey Rosenfeld
    • Related Report
      2018 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] Structural effects on the antigen-antibody interaction: Insight from molecular dynamics simulations of biopolymers2018

    • Author(s)
      Takefumi Yamashita
    • Organizer
      14th International Conference of Computational Methods in Sciences and Engineering (CC symposium of ICCMSE 2017)(Thessaloniki, Greece / Invited lecture)
    • Related Report
      2017 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] 分子動力学シミュレーションによる材料高分子の研究: 熱硬化性樹脂の高精度モデリング2018

    • Author(s)
      山下雄史
    • Organizer
      第8回 NTChem ワークショップ
    • Related Report
      2017 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] flat function の高階導関数について2018

    • Author(s)
      児玉大樹
    • Organizer
      早稲田幾何学的トポロジーセミナー, 早稲田大学
    • Related Report
      2017 Research-status Report
  • [Presentation] 分子動力学計算による抗原抗体複合体の形成過程の研究2017

    • Author(s)
      山下雄史, 高松佑一郎
    • Organizer
      日本化学会春季年会
    • Place of Presentation
      慶応義塾大学(神奈川県横浜市)
    • Year and Date
      2017-03-16
    • Related Report
      2016 Research-status Report
  • [Presentation] Molecular Dynamics Analysis of Protein Complex Structures2017

    • Author(s)
      Takefumi Yamashita
    • Organizer
      10th International Conference on Computational Physics (ICCP10)
    • Place of Presentation
      Macau, China
    • Year and Date
      2017-01-16
    • Related Report
      2016 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] A Molecular Dynamics Study on Antigen-Antibody Recognition2017

    • Author(s)
      Takefumi Yamashita
    • Organizer
      13th International Conference of Computational Methods in Sciences and Engineering (CC symposium of ICCMSE 2017)(Thessaloniki, Greece / Invited lecture)
    • Related Report
      2017 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] 分子動力学シミュレーションによる生体高分子の研究:RNAへの展開の現状と可能性2017

    • Author(s)
      山下雄史
    • Organizer
      2017年度生命科学系学会合同年次大会(ConBio2017)ワークショップ
    • Related Report
      2017 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] 生体分子のダイナミクスと機能:分子動力学シミュレーションの非コードRNA研究ツールとしての可能性2017

    • Author(s)
      山下雄史
    • Organizer
      一般財団法人バイオインダストリー協会主催"未来へのバイオ技術" 勉強会「長鎖非コードRNA研究の進歩と可能性」
    • Related Report
      2017 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] 分子動力学シミュレーションによるタンパク質の分子認識の研究:分子デザインへの挑戦2017

    • Author(s)
      山下雄史
    • Organizer
      量子系分子科学セミナー(理化学研究所計算科学研究機構)
    • Related Report
      2017 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] Molecular Environment effects on the protein structure: Molecular dynamics studies on the antigen-antibody interface2017

    • Author(s)
      Takefumi Yamashita
    • Organizer
      生物物理学会(Symposium: Molecular-Level Analysis of Environment Effect toward Tuning of Protein Structure and Function)
    • Related Report
      2017 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] 分子動力学計算による抗原と抗体の結合過程の研究2017

    • Author(s)
      山下 雄史・高松 佑一郎
    • Organizer
      分子科学討論会
    • Related Report
      2017 Research-status Report
  • [Presentation] flat function についての考察2017

    • Author(s)
      児玉大樹
    • Organizer
      玉原トポロジー・幾何セミナー, 東京大学玉原国際セミナーハウス
    • Related Report
      2017 Research-status Report
  • [Presentation] flat function の高階導関数について2017

    • Author(s)
      児玉大樹
    • Organizer
      「葉層構造と微分同相群2017 研究集会」Foliations and Diffeomorphism Groups 2017, 東京大学玉原国際セミナーハウス
    • Related Report
      2017 Research-status Report
  • [Presentation] On Quantitative Understanding on Antigen-Antibody Interaction through All-atom Molecular Dynamics Simulations2017

    • Author(s)
      Takefumi Yamashita
    • Organizer
      3rd Symposium on Biophysics Postgraduate Research in Hong Kong
    • Place of Presentation
      Hong Kong, China
    • Related Report
      2016 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] (RNAの)平面図とarc diagram2017

    • Author(s)
      児玉大樹
    • Organizer
      生命動態とその数理
    • Place of Presentation
      島根県松江市
    • Related Report
      2016 Research-status Report
  • [Presentation] Advancement and challenge in the all-atom molecular dynamics simulation for biomolecular systems2016

    • Author(s)
      Takefumi Yamashita
    • 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
      2016-11-30
    • Related Report
      2016 Research-status Report
    • Invited
  • [Presentation] Molecular Dynamics Simulation of Biomolecules: Accuracy Improvement and Computational Conditions2016

    • Author(s)
      Takefumi Yamashita
    • Organizer
      12th International Conference of Computational Methods in Sciences and Engineering (CC symposium of ICCMSE 2016)
    • Place of Presentation
      Athens (Greek)
    • Year and Date
      2016-03-20
    • Related Report
      2015 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] 分子動力学シミュレーションと蛋白質-小分子相互作用2016

    • Author(s)
      山下雄史
    • Organizer
      第89回薬理学会年会 シンポジウム「計算科学的アプローチによる薬理学研究の新展開」
    • Place of Presentation
      横浜
    • Year and Date
      2016-03-11
    • Related Report
      2015 Research-status Report
    • Invited
  • [Presentation] Protein structure analysis and SO(3)2016

    • Author(s)
      児玉大樹
    • Organizer
      トポロジーとコンピュータ2016
    • Place of Presentation
      秋田県秋田市
    • Related Report
      2016 Research-status Report
  • [Remarks] 論文一覧

    • URL

      http://www.lsbm.org/?publication_category=tss_publications

    • Related Report
      2017 Research-status Report
  • [Remarks] 子シミュレーションを使った抗体設計

    • URL

      http://www.lsbm.org/2018/04/12/

    • Related Report
      2017 Research-status Report
  • [Remarks] 解説記事の月間アクセス数ランキングが1位に

    • URL

      http://www.lsbm.org/2018/02/09/

    • Related Report
      2017 Research-status Report

URL: 

Published: 2015-07-14   Modified: 2021-02-19  

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