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This article is part of the supplement: APBioNet – Fifth International Conference on Bioinformatics (InCoB2006)

Open Access Proceedings

Projections for fast protein structure retrieval

Sourangshu Bhattacharya1, Chiranjib Bhattacharyya12* and Nagasuma R Chandra2

Author Affiliations

1 Dept. of Computer Science and Automation, Indian Institute of Science, Bangalore – 560012, India

2 Bioinformatics Center, Indian Institute of Science, Bangalore – 560012, India

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BMC Bioinformatics 2006, 7(Suppl 5):S5  doi:10.1186/1471-2105-7-S5-S5

Published: 18 December 2006



In recent times, there has been an exponential rise in the number of protein structures in databases e.g. PDB. So, design of fast algorithms capable of querying such databases is becoming an increasingly important research issue. This paper reports an algorithm, motivated from spectral graph matching techniques, for retrieving protein structures similar to a query structure from a large protein structure database. Each protein structure is specified by the 3D coordinates of residues of the protein. The algorithm is based on a novel characterization of the residues, called projections, leading to a similarity measure between the residues of the two proteins. This measure is exploited to efficiently compute the optimal equivalences.


Experimental results show that, the current algorithm outperforms the state of the art on benchmark datasets in terms of speed without losing accuracy. Search results on SCOP 95% nonredundant database, for fold similarity with 5 proteins from different SCOP classes show that the current method performs competitively with the standard algorithm CE. The algorithm is also capable of detecting non-topological similarities between two proteins which is not possible with most of the state of the art tools like Dali.