PocketMatch (version 2.0): A parallel algorithm for the detection of structural similarities between protein ligand binding-sites

Nagarajan, Deepesh and Chandra, Nagasuma (2013) PocketMatch (version 2.0): A parallel algorithm for the detection of structural similarities between protein ligand binding-sites. In: National Conference on Parallel Computing Technologies (PARCOMPTECH), FEB 21-23, 2013, Bangalore, INDIA.

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Abstract

Knowledge of protein-ligand interactions is essential to understand several biological processes and important for applications ranging from understanding protein function to drug discovery and protein engineering. Here, we describe an algorithm for the comparison of three-dimensional ligand-binding sites in protein structures. A previously described algorithm, PocketMatch (version 1.0) is optimised, expanded, and MPI-enabled for parallel execution. PocketMatch (version 2.0) rapidly quantifies binding-site similarity based on structural descriptors such as residue nature and interatomic distances. Atomic-scale alignments may also be obtained from amino acid residue pairings generated. It allows an end-user to compute database-wide, all-to-all comparisons in a matter of hours. The use of our algorithm on a sample dataset, performance-analysis, and annotated source code is also included.

Item Type:	Conference Proceedings
Publisher:	IEEE
Additional Information:	Copyright for this article belongs to the IEEE, 345 E 47TH ST, NEW YORK, NY 10017 USA
Keywords:	Structural bioinformatics; 3D sub-structure matching; molecular recognition; drug-discovery
Department/Centre:	Division of Biological Sciences > Biochemistry
Date Deposited:	11 Jun 2014 10:34
Last Modified:	11 Jun 2014 10:34
URI:	http://eprints.iisc.ac.in/id/eprint/49207

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