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Conference Paper
Fast Protein Strucrure Alignment by Joining Similar Substructurte Pair
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- Authors
- Chan Yong Park, Sung Hee Park, Dae Hee Kim, Soo Jun Park, Man Kyu Sung, Chi Jung Hwang
- Issue Date
- 2006-01
- Citation
- European Conference on Computational Biology (EBBC) 2006, pp.1-11
- Language
- English
- Type
- Conference Paper
- Abstract
- This paper proposes a novel protein structure alignment algorithm and its application. Since the functions of protein may come from its structure, the method of measuring structural similarities between two proteins can infer their functional closeness. In this paper, we have proposed a 3D chain code for measuring local geometric similarity of protein and a back tracking algorithm for joining local similar substructure. The 3D chain code that is a sequence of direction vectors between the atoms in a protein represents a local similarity of protein. We have designed and implemented a protein alignment system based on the 3D chain code and backtracking algorithm to demonstrate that it could be effective in protein structure alignment. The protein structure alignment system shows fast alignment with precise results.
- KSP Keywords
- Alignment algorithm, Backtracking algorithm, Chain code, Geometric Similarity, Local similarity, Protein Structure Alignment, Structure Similarity Index measure(SSIM)