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Expansion of Protein Electronic Structure DB System

Research Project

Project/Area Number 17K00395
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section一般
Research Field Life / Health / Medical informatics
Research InstitutionThe University of Tokyo

Principal Investigator

Hirano Toshiyuki  東京大学, 生産技術研究所, 助教 (60451887)

Project Period (FY) 2017-04-01 – 2020-03-31
Project Status Completed (Fiscal Year 2019)
Budget Amount *help
¥4,420,000 (Direct Cost: ¥3,400,000、Indirect Cost: ¥1,020,000)
Fiscal Year 2019: ¥1,040,000 (Direct Cost: ¥800,000、Indirect Cost: ¥240,000)
Fiscal Year 2018: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000)
Fiscal Year 2017: ¥2,080,000 (Direct Cost: ¥1,600,000、Indirect Cost: ¥480,000)
Keywordsタンパク質 / 電子状態 / 量子化学 / 電子状態計算 / 密度汎関数法 / 波動関数 / データベース / 生体生命情報学 / 蛋白質 / ハイパフォーマンス・コンピューティング / シミュレーション工学 / 物性理論
Outline of Final Research Achievements

In the protein electronic state calculation, we have improved the speed and efficiency of the electronic state calculation, and the structure of the calculation and the automation of the electronic state calculation based on the QCLO method: the electronic state calculation was accelerated by the GPU, and achieved with the limited resources of the memory-mapped file. We have developed an interaction analysis tool based on electronic state calculations and confirmed its usefulness in small-scale protein experiments.
The developed source code has been available on the Internet.

Academic Significance and Societal Importance of the Research Achievements

実験的に得られたタンパク質構造をもとに、タンパク質電子状態データベースの構築・拡張をおこなうため、タンパク質電子状態計算をより自動化し、省力化する研究開発を行った。タンパク質電子状態計算を高速化・効率化し、自動計算の簡略化・機能追加を行った。相互作用解析機能を追加し、基質やアミノ酸残基間の相互作用を可視化することができるようになった。
開発したソースコードはインターネット上に公開済みである。

Report

(4 results)
  • 2019 Annual Research Report   Final Research Report ( PDF )
  • 2018 Research-status Report
  • 2017 Research-status Report
  • Research Products

    (22 results)

All 2020 2019 2018 2017 Other

All Journal Article (4 results) (of which Peer Reviewed: 3 results,  Open Access: 1 results) Presentation (15 results) (of which Int'l Joint Research: 7 results,  Invited: 3 results) Remarks (3 results)

  • [Journal Article] Recent progress of protein canonical molecular orbital calculation by the third generation density functional method2019

    • Author(s)
      Hirano Toshiyuki、Sato Fumitoshi
    • Journal Title

      AIP Conference Proceedings

      Volume: 2186 Pages: 030009-030009

    • DOI

      10.1063/1.5137920

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Study on the Cloud-like Visualization Model of Protein Molecule Orbitals by the Rejection Method2018

    • Author(s)
      EGUCHI Haruki、HIRANO Toshiyuki、SATO Fumitoshi
    • Journal Title

      Journal of Computer Chemistry, Japan

      Volume: 17 Issue: 5 Pages: 189-192

    • DOI

      10.2477/jccj.2018-0062

    • NAID

      130007596235

    • ISSN
      1347-1767, 1347-3824
    • Related Report
      2018 Research-status Report
    • Open Access
  • [Journal Article] 大規模分子設計における電子状態計算法と期待2018

    • Author(s)
      平野敏行, 佐藤文俊
    • Journal Title

      放電研究

      Volume: 61 Pages: 13-18

    • Related Report
      2018 Research-status Report
    • Peer Reviewed
  • [Journal Article] Study of high-performance canonical molecular orbitals calculation for proteins2017

    • Author(s)
      Hirano Toshiyuki、Sato Fumitoshi
    • Journal Title

      AIP Conference Proceedings

      Volume: 1906 Pages: 030019-030019

    • DOI

      10.1063/1.5012298

    • Related Report
      2017 Research-status Report
    • Peer Reviewed
  • [Presentation] Study of interaction energy analysis of proteins by canonical Kohn-Sham molecular orbital calculation2020

    • Author(s)
      T. Hirano, F. Sato
    • Organizer
      The 60th Sanibel Symposium
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Interaction energy analysis based on canonical Kohn-Sham molecular orbital calculation of protein2019

    • Author(s)
      T. Hirano, F. Sato
    • Organizer
      DFT2019
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Recent Progress of Protein Canonical Molecular Orbital Calculation by the Third Generation Density Functional Method2019

    • Author(s)
      T. Hirano, F. Sato
    • Organizer
      ICCMSE2019
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] Analyzing intramolecular interaction using canonical Kohn-Sham molecular orbital calculation in protein2019

    • Author(s)
      平野敏行, 佐藤文俊
    • Organizer
      CBI学会2019年大会
    • Related Report
      2019 Annual Research Report
  • [Presentation] タンパク質カノニカル分子軌道計算における相互作用解析の研究2019

    • Author(s)
      平野敏行, 佐藤文俊
    • Organizer
      第13回分子科学討論会
    • Related Report
      2019 Annual Research Report
  • [Presentation] インスリン様成長因子1の電子状態の研究2019

    • Author(s)
      佐々木光, 平野敏行, 佐藤文俊
    • Organizer
      第13回分子科学討論会
    • Related Report
      2019 Annual Research Report
  • [Presentation] GPU acceleration of a canonical molecular orbital calculation program by the third-generation density-functional-theory-based method2019

    • Author(s)
      T. Hirano, F. Sato
    • Organizer
      The 59th Sanibel Symposium
    • Related Report
      2018 Research-status Report
    • Int'l Joint Research
  • [Presentation] Automated Canonical Molecular Orbital Calculation Engine for Protein: ProteinDF/QCLObot2018

    • Author(s)
      T. Hirano, F. Sato
    • Organizer
      16th international congress of quantum chemistry
    • Related Report
      2018 Research-status Report
    • Int'l Joint Research
  • [Presentation] 雲状モデルによるタンパク質分子軌道の新規可視化手法の研究2018

    • Author(s)
      江口晴輝, 平野敏行, 佐藤文俊
    • Organizer
      日本コンピュータ化学会 2018秋季年会
    • Related Report
      2018 Research-status Report
  • [Presentation] GPUを用いた大規模電子状態計算プログラムProteinDFの高速化2018

    • Author(s)
      平野敏行, 佐藤文俊
    • Organizer
      第12回分子科学討論会
    • Related Report
      2018 Research-status Report
  • [Presentation] Development of Molecular Orbitals Calculation Applications for Proteins2018

    • Author(s)
      Toshiyuki Hirano, Fumitoshi Sato
    • Organizer
      International Workshop on Massively Parallel Programming for Quantum Chemistry and Physics 2018
    • Related Report
      2017 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] Electronic structure of the active site on glucose oxidase by using canonical molecular orbital calculation2018

    • Author(s)
      Toshiyuki Hirano, Fumitoshi Sato
    • Organizer
      The 58th Sanibel Symposium
    • Related Report
      2017 Research-status Report
    • Int'l Joint Research
  • [Presentation] カノニカル分子軌道計算によるインフルエンザM2タンパク質の電子構造2017

    • Author(s)
      平野敏行, 佐藤文俊
    • Organizer
      分子科学討論会2017
    • Related Report
      2017 Research-status Report
  • [Presentation] QCLObot: an automation engine of canonical MO calculation in proteins2017

    • Author(s)
      Toshiyuki Hirano, Fumitoshi Sato
    • Organizer
      CBI学会2017年大会
    • Related Report
      2017 Research-status Report
  • [Presentation] Study of High-Performance Canonical Molecular Orbitals Calculation for Proteins2017

    • Author(s)
      Toshiyuki HIRANO, Fumitoshi SATO
    • Organizer
      International symposium: Computational Chemistry (CC) in ICCMSE2017
    • Related Report
      2017 Research-status Report
    • Int'l Joint Research / Invited
  • [Remarks] ProteinDF

    • URL

      https://github.com/ProteinDF/ProteinDF

    • Related Report
      2019 Annual Research Report 2018 Research-status Report
  • [Remarks] QCLObot

    • URL

      https://github.com/ProteinDF/QCLObot

    • Related Report
      2019 Annual Research Report 2018 Research-status Report
  • [Remarks] ProteinDF software package

    • URL

      https://proteindf.github.io/

    • Related Report
      2017 Research-status Report

URL: 

Published: 2017-04-28   Modified: 2021-02-19  

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