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. 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. Protein structure comparison is crucial for understanding protein evolution, architecture and function [1] . The Protein Data Bank (PDB) database [2], a public repository for macromolecule structure data, is a rapidly growing database which currently (as of 4 Aug 2009) contains structural information of 59,330 proteins. The steady growth of the PDB is now beginning to place considerable computational demands on queries which search the entire database, a routine task for determining structural protein similarities. There are a number of existing techniques to compare protein structures: Methods based on structural
A fast protein comparison algorithm IR Tableau was developed by Zhang et al. for protein retrieval purposes in REF , which leveraged the tableau representation to compare protein tertiary structures.
A fast indexing approach for protein structure comparison
BMC Bioinformatics
BMC Bioinformatics
Computer Science Medicine