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Please use this identifier to cite or link to this item: http://dspace.library.iitb.ac.in/jspui/handle/10054/941

Title: Parameterization and classification of the protein universe via geometric techniques
Authors: TENDULKAR, ASHISH V
WANGIKAR, PRAMOD P
SOHONI, MILIND
SAMANT, VIVEKANAND V
MONE, CHETAN Y
Keywords: classification
enzymes
proteins
inhibitors
Issue Date: 2003
Publisher: Elsevier
Citation: Journal of Molecular Biology 334(1), 157-172
Abstract: We present a scheme for the classification of 3487 non-redundant protein structures into 1207 non-hierarchical clusters by using recurring structural patterns of three to six amino acids as keys of classification. This results in several signature patterns, which seem to decide membership of a protein in a functional category. The patterns provide clues to the key residues involved in functional sites as well as in protein–protein interaction. The discovered patterns include a “glutamate double bridge” of superoxide dismutase, the functional interface of the serine protease and inhibitor, interface of homo/hetero dimers, and functional sites of several enzyme families. We use geometric invariants to decide superimposability of structural patterns. This allows the parameterization of patterns and discovery of recurring patterns via clustering. The geometric invariant-based approach eliminates the computationally explosive step of pair-wise comparison of structures. The results provide a vast resource for the biologists for experimental validation of the proposed functional sites, and for the design of synthetic enzymes, inhibitors and drugs.
URI: http://dx.doi.org/10.1016/j.jmb.2003.09.021
http://hdl.handle.net/10054/941
http://dspace.library.iitb.ac.in/xmlui/handle/10054/941
ISSN: 0022-2836
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