Structural similarity between proteins gives us insights on the evolutionary relationship between proteins which have low sequence similarity. In this paper, we present a novel approach called STSA for non-sequential pair-wise structural alignment. Starting from an initial alignment, our approach iterates over a two-step process, a superposition step and an alignment step, until convergence. Given two superposed structures, we propose a novel greedy algorithm to construct both sequential and non-sequential alignments. The quality of STSA alignments is evident in the high agreement it has with the reference alignments in the challenging-to-align RPIC set. Moreover, on a dataset of 4410 protein pairs selected from the CATH database, STSA has a high sensitivity and high specificity values and is competitive with state-of-the-art alignment methods and gives longer alignments with lower rmsd. The STSA software along with the data sets will be made available on line at http://www.cs.rpi.edu/-zaki/software/STSA.
|Number of pages||12|
|Journal||Computational systems bioinformatics / Life Sciences Society. Computational Systems Bioinformatics Conference|
|Publication status||Published - 1 Dec 2008|
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