Iterative non-sequential protein structural alignment.

Saeed Salem, Mohammed J. Zaki

Research output: Contribution to journalArticle

3 Citations (Scopus)

Abstract

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.

Original languageEnglish
Pages (from-to)183-194
Number of pages12
JournalComputational systems bioinformatics / Life Sciences Society. Computational Systems Bioinformatics Conference
Volume7
Publication statusPublished - 1 Dec 2008
Externally publishedYes

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Software
Proteins
Databases
Sensitivity and Specificity
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ASJC Scopus subject areas

  • Medicine(all)

Cite this

Iterative non-sequential protein structural alignment. / Salem, Saeed; Zaki, Mohammed J.

In: Computational systems bioinformatics / Life Sciences Society. Computational Systems Bioinformatics Conference, Vol. 7, 01.12.2008, p. 183-194.

Research output: Contribution to journalArticle

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