Projections for fast protein structure retrieval

Background: 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. Results: 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...

• Type: Journal
• Year: 2006
• Where: BMCBI
• Authors: Sourangshu Bhattacharya, Chiranjib Bhattacharyya, Nagasuma Chandra
• Keywords: Algorithms, BMCBI 2006, Protein, Protein Structure