Affiliation:
1. Institute for Infocomm Research, 21 Heng Mui Keng Terrace, Singapore 119613, Singapore
2. School of Computing, National University of Singapore, 3 Science Drive 2, Singapore 117543, Singapore
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 . .
Publisher
World Scientific Pub Co Pte Lt
Subject
Computer Science Applications,Molecular Biology,Biochemistry
Cited by
18 articles.
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