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Bioinformatics Advance Access originally published online on October 22, 2008
Bioinformatics 2008 24(24):2872-2879; doi:10.1093/bioinformatics/btn545
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© The Author 2008. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Integrated search and alignment of protein structures

Ahmet Sacan 1,2,*, I. Hakki Toroslu 1 and Hakan Ferhatosmanoglu 2,3

1Department of Computer Engineering, Middle East Technical University, Ankara, Turkey, 2Department of Computer, Science and Engineering and 3Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA

*To whom correspondence should be addressed.


  Abstract

Motivation: Identification and comparison of similar three-dimensional (3D) protein structures has become an even greater challenge in the face of the rapidly growing structure databases. Here, we introduce Vorometric, a new method that provides efficient search and alignment of a query protein against a database of protein structures. Voronoi contacts of the protein residues are enriched with the secondary structure information and a metric substitution matrix is developed to allow efficient indexing. The contact hits obtained from a distance-based indexing method are extended to obtain high-scoring segment pairs, which are then used to generate structural alignments.

Results: Vorometric is the first to address both search and alignment problems in the protein structure databases. The experimental results show that Vorometric is simultaneously effective in retrieving similar protein structures, producing high-quality structure alignments, and identifying cross-fold similarities. Vorometric outperforms current structure retrieval methods in search accuracy, while requiring com-parable running times. Furthermore, the structural superpositions produced are shown to have better quality and coverage, when compared with those of the popular structure alignment tools.

Availability: Vorometric is available as a web service at http://bio.cse.ohio-state.edu/Vorometric

Contact: sacan{at}cse.ohio-state.edu

Associate Editor: Anna Tramontano

Received on July 8, 2008; revised on September 26, 2008; accepted on October 19, 2008

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