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Improvement of target protein selection in NTDs based on large-scale protein structure prediction

Research Project

Project/Area Number 15K16082
Research Category

Grant-in-Aid for Young Scientists (B)

Allocation TypeMulti-year Fund
Research Field Life / Health / Medical informatics
Research InstitutionTokyo Institute of Technology

Principal Investigator

Ishida Takashi  東京工業大学, 情報理工学院, 准教授 (40508355)

Project Period (FY) 2015-04-01 – 2018-03-31
Project Status Completed (Fiscal Year 2017)
Budget Amount *help
¥3,900,000 (Direct Cost: ¥3,000,000、Indirect Cost: ¥900,000)
Fiscal Year 2016: ¥1,690,000 (Direct Cost: ¥1,300,000、Indirect Cost: ¥390,000)
Fiscal Year 2015: ¥2,210,000 (Direct Cost: ¥1,700,000、Indirect Cost: ¥510,000)
Keywordsトリパノソーマ寄生原虫症 / タンパク質立体構造予測 / 適合性フィードバック / 創薬標的タンパク質選定 / 顧みられない熱帯病 / シャーガス病 / 創薬標的タンパク質選択 / ランキング学習 / タンパク質ポケット探索 / タンパク質立体構造
Outline of Final Research Achievements

We constructed protein structure models for whole proteins encoded on genome of trypanosoma cruzi, which is a pathogenic agent of Chagas' disease, by using homology modeling technique. We also developed web-interface for accessing those structure models, and enabled drug discovery researchers to find more suitable target using protein structure information. In addition, we developed a new system to help the user find their demanded targets more efficiently based on relevance feedback and learning-to-rank.

Report

(4 results)
  • 2017 Annual Research Report   Final Research Report ( PDF )
  • 2016 Research-status Report
  • 2015 Research-status Report
  • Research Products

    (8 results)

All 2017 2016

All Journal Article (2 results) (of which Peer Reviewed: 2 results,  Open Access: 2 results,  Acknowledgement Compliant: 1 results) Presentation (6 results)

  • [Journal Article] In silico, in vitro, X-ray crystallography, and integrated strategies for discovering spermidine synthase inhibitors for Chagas disease2017

    • Author(s)
      Yoshino Ryunosuke、Yasuo Nobuaki、Hagiwara Yohsuke、Ishida Takashi、Inaoka Daniel Ken、Amano Yasushi、Tateishi Yukihiro、Ohno Kazuki、Namatame Ichiji、Niimi Tatsuya、Orita Masaya、Kita Kiyoshi、Akiyama Yutaka、Sekijima Masakazu
    • Journal Title

      Scientific Reports

      Volume: 7 Issue: 1 Pages: 1-9

    • DOI

      10.1038/s41598-017-06411-9

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Spresso: An ultrafast compound pre-screening method based on compound decomposition2017

    • Author(s)
      Keisuke Yanagisawa, Shunta Komine, Shogo D. Suzuki, Masahito Ohue, Takashi Ishida, Yutaka Akiyama
    • Journal Title

      Bioinformatics

      Volume: 印刷中 Issue: 23 Pages: 3836-3843

    • DOI

      10.1093/bioinformatics/btx178

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Presentation] 薬剤標的タンパク質選定支援に向けた立体構造上での株間変異情報表示システムの開発2017

    • Author(s)
      大石智博,石田貴士
    • Organizer
      情報処理学会 第50回バイオ情報学研究会
    • Related Report
      2017 Annual Research Report
  • [Presentation] 適合性フィードバックを用いたトリパノソーマ原虫症薬剤標的タンパク質選定の改良2017

    • Author(s)
      曽我 光瑛,石田 貴士
    • Organizer
      情報処理学会 第53回バイオ情報学研究会
    • Related Report
      2017 Annual Research Report
  • [Presentation] Prediction of Protein-Ligand Binding Sites Using 3D Convolutional Neural Networks2016

    • Author(s)
      Naoto Kakami, Takashi Ishida
    • Organizer
      Informatics in Biology, Medicine and Pharmacology 2016 (IIBMP2016)
    • Place of Presentation
      Tokyo
    • Related Report
      2016 Research-status Report
  • [Presentation] Improvement of NTDs drug target protein selection by learning to rank2016

    • Author(s)
      Mitsuaki Soga, Takashi Ishida
    • Organizer
      Informatics in Biology, Medicine and Pharmacology 2016 (IIBMP2016)
    • Place of Presentation
      Tokyo
    • Related Report
      2016 Research-status Report
  • [Presentation] ランク学習を用いたNTDs薬剤標的タンパク質候補選択の改良2016

    • Author(s)
      曽我光瑛, 石田貴士
    • Organizer
      情報処理学会 第46回バイオ情報学研究会
    • Place of Presentation
      沖縄
    • Related Report
      2016 Research-status Report
  • [Presentation] 3次元畳み込みニューラルネットワークを用いたタンパク質リガンド結合ポケットの予測2016

    • Author(s)
      各務直人, 石田貴士
    • Organizer
      情報処理学会 第46回バイオ情報学研究会
    • Place of Presentation
      沖縄
    • Related Report
      2016 Research-status Report

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Published: 2015-04-16   Modified: 2019-03-29  

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