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Prediction of Residues with Key Interactions with Ligands Based on Receptor Environmental Properties

Research Project

Project/Area Number 26870848
Research Category

Grant-in-Aid for Young Scientists (B)

Allocation TypeMulti-year Fund
Research Field Physical pharmacy
Life / Health / Medical informatics
Research InstitutionInstitute of Physical and Chemical Research

Principal Investigator

Takaya Daisuke  国立研究開発法人理化学研究所, ライフサイエンス技術基盤研究センター, 研究員 (50571395)

Project Period (FY) 2014-04-01 – 2016-03-31
Project Status Completed (Fiscal Year 2015)
Budget Amount *help
¥3,900,000 (Direct Cost: ¥3,000,000、Indirect Cost: ¥900,000)
Fiscal Year 2015: ¥650,000 (Direct Cost: ¥500,000、Indirect Cost: ¥150,000)
Fiscal Year 2014: ¥3,250,000 (Direct Cost: ¥2,500,000、Indirect Cost: ¥750,000)
Keywordsタンパク質ーリガンド間相互作用 / 評価関数 / 機械学習 / ドッキング / タンパク質ーリガンド間相互作用解 / 相互作用記述子 / タンパク質 / リガンド
Outline of Final Research Achievements

In SBDD, protein-ligand docking is a powerful method to identify its inhibitors. We focused on residues involving in key interaction(s) such as H-bonds, ionic bonds, tight hydrophobic contact with ligands. If a prediction method for importance measure of the binding site residues is given beforehand, we could use the rank for the do rescoring and filtering. In this study, we newly set a purpose to develop prediction methods to quantify the importance of residues with the key interaction(s) around the pockets.
As a result of this study, interaction energies of probe molecules and information of amino acid were selected as descriptors and these descriptors were used for constructing prediction models. Moreover, two kinds of validation using data set based on experimental protein-ligand structures in PDB were performed to evaluate the prediction model using performance indicators such as ROC score and correlation coefficient.

Report

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

    (1 results)

All 2015

All Presentation (1 results)

  • [Presentation] Prediction of Residues with Key Interactions with Ligands Based on Receptor Environmental Properties2015

    • Author(s)
      Daisuke Takaya, Honma Teruki
    • Organizer
      CBI学会2015年大会
    • Place of Presentation
      タワーホール船堀・江戸川区・東京都
    • Year and Date
      2015-10-27
    • Related Report
      2015 Annual Research Report

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

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