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Datamining approach for protein-ligand interaction mediated by hydration water

Research Project

Project/Area Number 25650050
Research Category

Grant-in-Aid for Challenging Exploratory Research

Allocation TypeMulti-year Fund
Research Field Biophysics
Research InstitutionJapan Advanced Institute of Science and Technology

Principal Investigator

Mizukami Taku  北陸先端科学技術大学院大学, 先端科学技術研究科, 助教 (50270955)

Project Period (FY) 2013-04-01 – 2017-03-31
Project Status Completed (Fiscal Year 2016)
Budget Amount *help
¥2,080,000 (Direct Cost: ¥1,600,000、Indirect Cost: ¥480,000)
Fiscal Year 2015: ¥650,000 (Direct Cost: ¥500,000、Indirect Cost: ¥150,000)
Fiscal Year 2014: ¥780,000 (Direct Cost: ¥600,000、Indirect Cost: ¥180,000)
Fiscal Year 2013: ¥650,000 (Direct Cost: ¥500,000、Indirect Cost: ¥150,000)
Keywordsタンパク質 / 水和 / 分子動力学計算 / データマイニング / 特徴空間 / 機械学習 / 蛋白質 / 分子動力学 / ドッキング / Lasso正則化
Outline of Final Research Achievements

The motivation of the research is 1) visualization of hydration water defined by data-mining method, and 2) estimation of hydration effect by means of solvation free energy.
We founded a system for mining water behavior by means of the mixture model from MD simulation data. It detected a strong correlation between solvation free energy and hydration water behavior that enables a prediction of free energy.
The machine learning and prediction system was build with the combination of three methods, linear model, clustering and a new descriptor that was designed by accounting the multi-body interaction between atoms. Application of the machine for the small-scale solution / molecular systems resulted in a more detailed prediction for the energies.

Report

(5 results)
  • 2016 Annual Research Report   Final Research Report ( PDF )
  • 2015 Research-status Report
  • 2014 Research-status Report
  • 2013 Research-status Report
  • Research Products

    (14 results)

All 2017 2016 2015 2014 2013

All Journal Article (2 results) (of which Peer Reviewed: 2 results,  Open Access: 1 results) Presentation (12 results) (of which Int'l Joint Research: 3 results)

  • [Journal Article] Prediction of Solvation Free Energy of Proteins: Molecular Dynamics Simulation and QSPR Model Approach2015

    • Author(s)
      Sri R. Natasia, Hiroaki Saito, Taku Mizukami, Kazutomo Kawaguchi and Hidemi Nagao
    • Journal Title

      Recent Development in Computational Science

      Volume: 6 Pages: 100-111

    • Related Report
      2015 Research-status Report
    • Peer Reviewed
  • [Journal Article] Molecular Dynamics Study of Gramicidin A in Lipid Bilayer: Electrostatic Map and Ion Conduction2014

    • Author(s)
      Hiroaki SAITO, Masashi IWAYAMA, Kazutomo KAWAGUCHI, Taku MIZUKAMI, Takeshi MIYAKAWA, Masako TAKASU, and Hidemi NAGAO
    • Journal Title

      JPS Conf. Proc

      Volume: volume 1 Pages: 012053-012053

    • DOI

      10.7566/jpscp.1.012053

    • Related Report
      2014 Research-status Report
    • Peer Reviewed / Open Access
  • [Presentation] Machine-learning approach for behavior of hydration water; A pathway to discovery and prediction for biophysical and physiological properties of protein2017

    • Author(s)
      Taku Mizukami, Nguyen Viet Cuong, Pham Tien Lam, Dam Heiu Chi
    • Organizer
      International Symposium on Biophysics of Rhodopsins Celebrating Prof. Yoshinori Shichida
    • Place of Presentation
      京都大学(京都府京都市)
    • Year and Date
      2017-05-11
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research
  • [Presentation] 機械学習によるタンパク質親水/疎水表面における水分子の動的振る舞いの解析2016

    • Author(s)
      水上 卓, Viet Cuong Nguyen, Ho Tu Bao, and Dam Hieu Chi
    • Organizer
      生物物理学会 第54回年会
    • Place of Presentation
      つくば国際会議場(茨城県つくば市)
    • Year and Date
      2016-11-25
    • Related Report
      2016 Annual Research Report
  • [Presentation] アンサンブルドッキングを用いたCYP1A2化合物の代謝部位予測2016

    • Author(s)
      齋藤 大明, 水上 卓, 平野 秀典, 大塚 教雄, 沖本 憲明, 泰地 真弘人
    • Organizer
      生物物理学会 第54回年会
    • Place of Presentation
      つくば国際会議場(茨城県つくば市)
    • Year and Date
      2016-11-25
    • Related Report
      2016 Annual Research Report
  • [Presentation] Simulation-based data-mining approach for the protein hydration water behavior2015

    • Author(s)
      Taku Mizukami, Nguyen Viet Cuong, Ho Tu Bao, and Dam Hieu Chi
    • Organizer
      Pacifichem2015
    • Place of Presentation
      USA, Honolulu
    • Year and Date
      2015-12-14
    • Related Report
      2015 Research-status Report
    • Int'l Joint Research
  • [Presentation] シミュレーション・データマイニングによるリガンド結合系における水分子の振る舞い2015

    • Author(s)
      水上 卓, グェン ベトクン, ホー ツーバオ, ダム ヒョウチ
    • Organizer
      生物物理学会年会
    • Place of Presentation
      石川県金沢市,金沢大学
    • Year and Date
      2015-11-25
    • Related Report
      2015 Research-status Report
  • [Presentation] Hydration Water Behavior Characterization by Simulation-Based Data-Mining Approach2015

    • Author(s)
      Taku Mizukami, Nguyen Viet Cuong, Ho Tu Bao, and Dam Hieu Chi
    • Organizer
      ACCMS8 (Conference of Asian Consortium on Computational Materials Science)
    • Place of Presentation
      NTUST,Taipei, Taiwan
    • Year and Date
      2015-06-16 – 2015-06-18
    • Related Report
      2014 Research-status Report
  • [Presentation] Hydration Water Behavior Characterization by Simulation-Based Data-Mining Approach2015

    • Author(s)
      Taku Mizukami, Viet Cuong Nguen, Tu Bao Ho, Hieu Chi Dam
    • Organizer
      The 8th Conference of the Asian Consortium on Computational Materials Science (ACCMS-8)
    • Place of Presentation
      台湾,台北市
    • Year and Date
      2015-06-16
    • Related Report
      2015 Research-status Report
    • Int'l Joint Research
  • [Presentation] Hydration water behavior classified by mixture model : Simulation data-mining approach2014

    • Author(s)
      Taku Mizukami, Viet Cuong Nguen, Tu Bao Ho, Hieu Chi Dam
    • Organizer
      第52回日本生物物理学会年会
    • Place of Presentation
      北海道札幌市・札幌コンベンションセンター
    • Year and Date
      2014-09-13 – 2014-09-15
    • Related Report
      2014 Research-status Report
  • [Presentation] A novel category of protein hydration water classified by simulated data mining approach2013

    • Author(s)
      Taku Mizukami, Ayumu Sugiyama, Dam Hieu Chi, Ho Tu Bao
    • Organizer
      ACCMS-7
    • Place of Presentation
      Thailand, Korat
    • Related Report
      2013 Research-status Report
  • [Presentation] Structural analysis of protein hydration water by means of sparse model2013

    • Author(s)
      水上 卓, 杉山 歩, 川崎 隆史, 高木 啓行, ホー・ツー・バオ, ダム・ヒョウ・チ
    • Organizer
      第7回分子科学討論会
    • Place of Presentation
      京都テルサ
    • Related Report
      2013 Research-status Report
  • [Presentation] L1型正則化線形回帰モデルを用いたシミュレーションデータからの二元合金の物性予測2013

    • Author(s)
      鈴木 大輔,川崎 隆史, 杉山 歩,水上 卓,Dam Hieu Chi, Ho Tu Bao
    • Organizer
      第7回分子科学討論会
    • Place of Presentation
      京都テルサ
    • Related Report
      2013 Research-status Report
  • [Presentation] シミュレーション・データマイニングアプローチによる蛋白質ドッキング過程における水和水ダイナミクス2013

    • Author(s)
      水上 卓, 杉山 歩, ホー・ツー・バオ, ダム・ヒョウ・チ
    • Organizer
      生物物理学会 第51回年会
    • Place of Presentation
      京都国際会議場
    • Related Report
      2013 Research-status Report

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Published: 2014-07-25   Modified: 2019-07-29  

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