This article is part of the supplement: Selected articles from the Eighth Asia-Pacific Bioinformatics Conference (APBC 2010)
Research
A fast indexing approach for protein structure comparison
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* Corresponding author: Lei Zhang lzhan@csse.unimelb.edu.au
1 National ICT Australia (NICTA) Victoria Research Laboratory at The University of Melbourne, Melbourne, Victoria, Australia
2 Department of Computer Science and Software Engineering, The University of Melbourne, Melbourne, Victoria 3010, Australia
BMC Bioinformatics 2010, 11(Suppl 1):S46 doi:10.1186/1471-2105-11-S1-S46
Published: 18 January 2010Abstract
Background
Protein structure comparison is a fundamental task in structural biology. While the number of known protein structures has grown rapidly over the last decade, searching a large database of protein structures is still relatively slow using existing methods. There is a need for new techniques which can rapidly compare protein structures, whilst maintaining high matching accuracy.
Results
We have developed IR Tableau, a fast protein comparison algorithm, which leverages the tableau representation to compare protein tertiary structures. IR tableau compares tableaux using information retrieval style feature indexing techniques. Experimental analysis on the ASTRAL SCOP protein structural domain database demonstrates that IR Tableau achieves two orders of magnitude speedup over the search times of existing methods, while producing search results of comparable accuracy.
Conclusion
We show that it is possible to obtain very significant speedups for the protein structure comparison problem, by employing an information retrieval style approach for indexing proteins. The comparison accuracy achieved is also strong, thus opening the way for large scale processing of very large protein structure databases.