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http://dx.doi.org/10.3745/KIPSTB.2009.16B.5.359

A Study of Flexible Protein Structure Alignment Using Three Dimensional Local Similarities  

Park, Chan-Yong (한국전자통신연구원 라이프인포매틱스팀)
Hwang, Chi-Jung (충남대학교 전기정보통신공학부)
Publication Information
The KIPS Transactions:PartB / v.16B, no.5, 2009 , pp. 359-366 More about this Journal
Abstract
Analysis of 3-dimensional (3D) protein structure plays an important role of structural bioinformatics. The protein structure alignment is the main subjects of the structural bioinformatics and the most fundamental problem. Protein Structures are flexible and undergo structural changes as part of their function, and most existing protein structure comparison methods treat them as rigid bodies, which may lead to incorrect alignment. We present a new method that carries out the flexible structure alignment by means of finding SSPs(Similar Substructure Pairs) and flexible points of the protein. In order to find SSPs, we encode the coordinates of atoms in the backbone of protein into RDA(Relative Direction Angle) using local similarity of protein structure. We connect the SSPs with Floyd-Warshall algorithm and make compatible SSPs. We compare the two compatible SSPs and find optimal flexible point in the protein. On our well defined performance experiment, 68 benchmark data set is used and our method is better than three widely used methods (DALI, CE, FATCAT) in terms of alignment accuracy.
Keywords
Protein Structure Alignment; Bioinformatics; RDA; Graph Optimization;
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