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Development of an intelligent dynamic docking pipeline for improving molecular docking simulations.

Research Project

Project/Area Number 26730152
Research Category

Grant-in-Aid for Young Scientists (B)

Allocation TypeMulti-year Fund
Research Field Life / Health / Medical informatics
Research InstitutionOkinawa Institute of Science and Technology Graduate University

Principal Investigator

Hsin Kun-Yi  沖縄科学技術大学院大学, その他の研究科, 研究員 (60604155)

Project Period (FY) 2014-04-01 – 2016-03-31
Project Status Completed (Fiscal Year 2015)
Budget Amount *help
¥3,770,000 (Direct Cost: ¥2,900,000、Indirect Cost: ¥870,000)
Fiscal Year 2015: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000)
Fiscal Year 2014: ¥2,600,000 (Direct Cost: ¥2,000,000、Indirect Cost: ¥600,000)
KeywordsDocking Simulation / Molecular Dynamics / Network Pharmacology / Machine Learning / Molecular Interaction / Drug Discovery
Outline of Final Research Achievements

In order to precisely and efficiently predict the binding potentials of test compounds against proteins involved in a molecular pathway, we have developed a network pharmacology-based prediction pipeline. By assessing the correlations between the prediction scores and the experimental binding affinities, our prediction method shown a good performance in predicting the binding potentials (R >0.8).
Additionally, we predicted the selectivity of various kinase inhibitors by comparing with known bioassay results, showing a good consistency. The relevant research results have been published on high-impact journals. We have also applied it to several joined projects helping collaborators, including those in Systems Biology Institute (SBI, Tokyo) and The University of Tokyo (IMSUT), to identify druggable molecules. A publicly accessible website called “systemsDock” (http://systemsdock.unit.oist.jp/) has been published, dedicating our achievements to the community of drug discovery.

Report

(3 results)
  • 2015 Annual Research Report   Final Research Report ( PDF )
  • 2014 Research-status Report
  • Research Products

    (14 results)

All 2016 2015 2014 Other

All Journal Article (3 results) (of which Int'l Joint Research: 3 results,  Peer Reviewed: 3 results,  Open Access: 3 results,  Acknowledgement Compliant: 1 results) Presentation (8 results) (of which Int'l Joint Research: 2 results,  Invited: 1 results) Remarks (2 results) Patent(Industrial Property Rights) (1 results) (of which Overseas: 1 results)

  • [Journal Article] systemsDock: a web server for network pharmacology-based prediction and analysis.2016

    • Author(s)
      Kun-Yi Hsin, Yukiko Matsuoka, Yoshiyuki Asai, Kyota Kamiyoshi, Tokiko Watanabe, Yoshihiro Kawaoka and Hiroaki Kitano
    • Journal Title

      Nucleic Acids Research

      Volume: . Issue: W1 Pages: 1-1

    • DOI

      10.1093/nar/gkw335

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] Identification of potential inhibitors based on compound proposal contest: Tyrosine-protein kinase Yes as a target2015

    • Author(s)
      Chiba S, Akiyama Y, Sekijima M.
    • Journal Title

      Scientific Reports

      Volume: 5 Issue: 1 Pages: 1-13

    • DOI

      10.1038/srep17209

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Application of machine leaning approaches in drug target identification and network pharmacology.2015

    • Author(s)
      Hsin, K. Y. Kitano, H., Matsuoka, Y. and Ghosh, S.
    • Journal Title

      IEEE

      Volume: . Pages: 219-219

    • DOI

      10.1109/iciibms.2015.7439493

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Presentation] Development of predictive machine leaning system in target protein identification and network pharmacology.2016

    • Author(s)
      Kun-Yi Hsin
    • Organizer
      Advances in Systems and Synthetic Biology 2016
    • Place of Presentation
      Evry, France
    • Year and Date
      2016-03-21
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Application of machine leaning approaches in drug target identification and network pharmacology2015

    • Author(s)
      Kun-Yi Hsin
    • Organizer
      International Conference on Intelligent Informatics and BioMedical Sciences (ICIIBMS 2015), Japan
    • Place of Presentation
      Okinawa, Japan
    • Year and Date
      2015-11-28
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Discovery of anti-influenza agents and drug targets using pathway map (FluMap) and computational approaches2015

    • Author(s)
      Kun-Yi Hsin
    • Organizer
      東京大学医科学研究所共同研究拠点成果報告会
    • Place of Presentation
      Tokyo, Japan
    • Year and Date
      2015-03-06
    • Related Report
      2014 Research-status Report
  • [Presentation] Combining machine learning systems and multiple docking simulations for network pharmacology2015

    • Author(s)
      Kun-Yi Hsin, Yukiko Matsuoka and Hiroaki Kitano
    • Organizer
      4th Negative Strand Virus Symposium (NSV-J)
    • Place of Presentation
      Okinawa, Japan
    • Year and Date
      2015-01-19 – 2015-01-21
    • Related Report
      2014 Research-status Report
  • [Presentation] Molecular Docking Simulations in the Era of Network Pharmacology2014

    • Author(s)
      Kun-Yi Hsin
    • Organizer
      第42回構造活性相関シンポジウム (日本薬学会-構造活性相関部会)
    • Place of Presentation
      Kumamoto, Japan
    • Year and Date
      2014-11-13 – 2014-11-14
    • Related Report
      2014 Research-status Report
    • Invited
  • [Presentation] High-Throughput Virtual Molecular Docking2014

    • Author(s)
      Kun-Yi Hsin and Hiroaki Kitano
    • Organizer
      BioJapan 2014, World Business Forum
    • Place of Presentation
      Yokohama, Japan
    • Year and Date
      2014-10-15 – 2014-10-17
    • Related Report
      2014 Research-status Report
  • [Presentation] Molecular Simulations for Network Pharmacology2014

    • Author(s)
      Kun-Yi Hsin, Samik Ghosh and Hiroaki Kitano
    • Organizer
      Symposium EuroQSAR - Understanding Chemical-Biological Interactions
    • Place of Presentation
      St. Petersburg, Russia
    • Year and Date
      2014-08-31 – 2014-09-04
    • Related Report
      2014 Research-status Report
  • [Presentation] Using machine learning systems and multiple docking simulations for network pharmacology making safer drugs2014

    • Author(s)
      Kun-Yi Hsin, Samik Ghosh and Hiroaki Kitano
    • Organizer
      Advances in Biomolecular Modelling and Simulations using CHARMM
    • Place of Presentation
      Dublin, Ireland
    • Year and Date
      2014-06-03 – 2014-06-06
    • Related Report
      2014 Research-status Report
  • [Remarks] systemDock, for network-based prediction.

    • URL

      http://systemsdock.unit.oist.jp/

    • Related Report
      2015 Annual Research Report
  • [Remarks] Intelligent Dynamic Docking Pipeline (IDDP)

    • URL

      http://docking.unit.oist.jp/

    • Related Report
      2014 Research-status Report
  • [Patent(Industrial Property Rights)] Interaction prediction device, interaction prediction method, and computer program product2014

    • Inventor(s)
      Kun-Yi Hsin, Hiroaki Kitano
    • Industrial Property Rights Holder
      Kun-Yi Hsin, Hiroaki Kitano
    • Industrial Property Rights Type
      特許
    • Filing Date
      2014-12-01
    • Related Report
      2014 Research-status Report
    • Overseas

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Published: 2014-04-04   Modified: 2017-05-10  

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