Identification of Domains and Domain Interface Residues in Multidomain Proteins from Graph Spectral Method

Sistla, Ramesh K and Brinda, KV and Vishveshwara, Saraswathi (2005) Identification of Domains and Domain Interface Residues in Multidomain Proteins from Graph Spectral Method. In: Proteins-structure Function and Bioinformatics, 59 (3). pp. 616-626.

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Abstract

We present a novel method for the identification of structural domains and domain interface residues in proteins by graph spectral method.This method converts the three-dimensional structure of the protein into a graph by using atomic coordinates from the PDB file.Domain definitions are obtained by constructing either a protein backbone graph or a protein side-chain graph. The graph is constructed based onthe interactions between amino acid residues in the three-dimensional structure of the proteins. The spectral parameters of such a graph contain information regarding the domains and subdomains in the protein structure. This is based on the fact that the interactions among amino acids are higher within a domain than across domains. This is evident in the spectra of the protein backbone and the side-chain graphs, thus differentiating the structural domains from one another. Further,residues that occur at the interface of two domains can also be easily identified from the spectra. This method is simple, elegant, and robust. Moreover, a single numeric computation yields both the domain definitions and the interface residues.

Item Type:	Journal Article
Publication:	Proteins-structure Function and Bioinformatics
Publisher:	Wiley-Liss
Additional Information:	Copyright for this article belongs to Wiley-Liss.
Keywords:	protein domain;domain interface;protein structure graph;eigen spectra;vector component
Department/Centre:	Division of Biological Sciences > Molecular Biophysics Unit
Date Deposited:	26 May 2005
Last Modified:	19 Sep 2010 04:19
URI:	http://eprints.iisc.ac.in/id/eprint/3249

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