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2013 National Conference on Parallel Computing Technologies (PARCOMPTECH) (2013)
Bangalore, India
Feb. 21, 2013 to Feb. 23, 2013
ISBN: 978-1-4799-1589-7
pp: 1-6
Deepesh Nagarajan , Biochemistry Department. Indian Institute of Science, Bangalore, India
Nagasuma Chandra , Biochemistry Department. Indian Institute of Science, Bangalore, India
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.
INDEX TERMS
drug-discovery, Structural bioinformatics, 3D sub-structure matching, molecular recognition
CITATION
Deepesh Nagarajan, Nagasuma Chandra, "PocketMatch (version 2.0): A parallel algorithm for the detection of structural similarities between protein ligand binding-sites", 2013 National Conference on Parallel Computing Technologies (PARCOMPTECH), vol. 00, no. , pp. 1-6, 2013, doi:10.1109/ParCompTech.2013.6621397
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