Development of a complex structure prediction method between proteins using binding free-energy as a scoring function

2015 Fiscal Year Final Research Report

• Project/Area Number: 25440070
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Multi-year Fund
• Section: 一般
• Research Field: Biophysics
• Research Institution: Institute of Physical and Chemical Research (2015); Osaka University (2013-2014)
• 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)
• Project Period (FY): 2013-04-01 – 2016-03-31
• 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

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.

Free Research Field

生物物理