| 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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| 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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