Development of a new De Novo protein structure prediction method based on a different approach of the fragment assembly method

2014 Fiscal Year Final Research Report

• Project/Area Number: 23770174
• Research Category: Grant-in-Aid for Young Scientists (B)
• Allocation Type: Multi-year Fund
• Research Field: Biophysics
• Research Institution: Nagoya University
• Principal Investigator: GEORGE Chikenji 名古屋大学, 工学(系)研究科(研究院), 助教 (10420366)
• Project Period (FY): 2011-04-28 – 2015-03-31
• Keywords: タンパク質 / 立体構造予測 / フラグメントアセンブリ法 / 構造アラインメント / non-sequential

Outline of Final Research Achievements

Protein structure prediction is one of the most important problems in biophysics. Although the fragment assembly method has been known as the most successful method, it has clear limitation. In this research project, we developed a new De Novo protein structure prediction method based on a different approach of the fragment assembly method. In this method, new fold structures are generated by permutation of secondary structures, and model qualities are assessed by physic-chemical energy function. We also developed several algorithms of structural bioinformatics, such as a non-sequential structure alignment algorithm and a program for detecting loop crossing. We performed protein structure prediction benchmark tests using the new method and found that our method outperformed the fragment assembly method for some targets.

Free Research Field

生物物理