GraProStr - Graphs of Protein Structures: A Tool for Constructing the Graphs and Generating Graph Parameters for Protein Structures
RESEARCH ARTICLE

GraProStr - Graphs of Protein Structures: A Tool for Constructing the Graphs and Generating Graph Parameters for Protein Structures

The Open Bioinformatics Journal 11 Feb 2011 RESEARCH ARTICLE DOI: 10.2174/1875036201105010053

Abstract

Protein structures can be represented as graphs/networks by defining the amino-acids as nodes and the noncovalent interactions as connections (edges). An analysis of such a graph provides valuable insights into the global structural properties, function, folding, and stability of proteins. Here we have created a webtool GraProStr to generate protein structure networks and analyze network parameters. Protein side-chain based, Cα/Cβ backbone based or proteinligand Graphs/Networks can be generated using GraProStr. The well tested tool is now made available to the scientific community for the first time. GraProStr is available online and can be accessed from http://vishgraph.mbu.iisc.ernet.in/GraProStr/index.html using any of the internet browsers (best viewed in Mozilla Firefox version ≥ 3.6). The webtool is written using Perl CGI and available using Apache Webserver. With its customizable definitions of protein structure networks and well defined network parameters, GraProStr can be a very useful tool for both theoretical and experimental elucidation of protein structures.

Keywords: Protein Structure Network, Non-covalent Interactions, Clusters, Hubs, Cliques, Communities.