Development of a complex structure prediction method between proteins using binding free-energy as a scoring function
| Project/Area Number |
25440070
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| Research Category |
Grant-in-Aid for Scientific Research (C)
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| Allocation Type | Multi-year Fund |
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| Section | 一般 |
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| Research Field |
Biophysics
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| Research Institution | Institute of Physical and Chemical Research (2015)
Osaka University (2013-2014) |
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Principal Investigator |
Kamiya Narutoshi 国立研究開発法人理化学研究所, 計算科学研究機構, 研究員 (80420462)
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| Project Period (FY) |
2013-04-01 – 2016-03-31
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| Project Status |
Completed (Fiscal Year 2015)
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| Budget Amount *help |
¥5,200,000 (Direct Cost: ¥4,000,000、Indirect Cost: ¥1,200,000)
Fiscal Year 2015: ¥910,000 (Direct Cost: ¥700,000、Indirect Cost: ¥210,000)
Fiscal Year 2014: ¥910,000 (Direct Cost: ¥700,000、Indirect Cost: ¥210,000)
Fiscal Year 2013: ¥3,380,000 (Direct Cost: ¥2,600,000、Indirect Cost: ¥780,000)
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| Keywords | 自由エネルギー / 分子動力学シミュレーション / 抗原抗体 / 立体構造予測 |
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| Outline of Final Research Achievements |
A computational method that can predict both the complex structure and the affinity between proteins such as antigen-antibody with high speed and accuracy has been developed. This method is composed of decoy generation by rough docking, followed by ranking of the decoys using the free-energy obtained from molecular dynamics simulation as a scoring function. We applied this method to PPARγ, which revealed that as the ligand dissociates, it passes near R288. Decoy sets of hemagglutinin-antibody and adenosine receptor-antibody were ranked by GB/SA scoring, where the near-native decoy was ranked within top 2. The binding free-energy calculation of hemagglutinin-antibody reproduced the experimental value better in comparison with the GB/SA method.
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Report
(4 results)
Research Products
(24 results)
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[Journal Article] NMR Characterization of the Interaction of the Endonuclease Domain of MutL with Divalent Metal Ions and ATP2014
Author(s)
Mizushima R, Kim JK, Suetake I, Tanaka H, Takai T, Kamiya N, Takano Y, Mishima Y, Tajima S, Goto Y, Fukui K, *Lee YH
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Journal Title
PLoS One
Volume: 9
Issue: 6
Pages: e98554-e98554
DOI
NAID
Related Report
Peer Reviewed / Open Access / Acknowledgement Compliant
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