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Title: MatAlign: Precise protein structure comparison by matrix alignment
Authors: Aung, Z.
Tan, K.-L. 
Keywords: Alignment quality criteria
Protein structure
Structural alignment
Structural classification
Issue Date: 2006
Citation: Aung, Z.,Tan, K.-L. (2006). MatAlign: Precise protein structure comparison by matrix alignment. Journal of Bioinformatics and Computational Biology 4 (6) : 1197-1216. ScholarBank@NUS Repository.
Abstract: We propose a detailed protein structure alignment method named "MatAlign". It is a two-step algorithm. Firstly, we represent 3D protein structures as 2D distance matrices, and align these matrices by means of dynamic programming in order to find the initially aligned residue pairs. Secondly, we refine the initial alignment iteratively into the optimal one according to an objective scoring function. We compare our method against DALI and CE, which are among the most accurate and the most widely used of the existing structural comparison tools. On the benchmark set of 68 protein structure pairs by Fischer et al., MatAlign provides better alignment results, according to four different criteria, than both DALI and CE in a majority of cases. MatAlign also performs as well in structural database search as DALI does, and much better than CE does. MatAlign is about two to three times faster than DALI, and has about the same speed as CE. The software and the supplementary information for this paper are available at © Imperial College Press.
Source Title: Journal of Bioinformatics and Computational Biology
ISSN: 02197200
DOI: 10.1142/S0219720006002417
Appears in Collections:Staff Publications

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