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

Abstract

Protein structures can be represented as graphs/networks by defining the amino-acids as nodes and the non-covalent 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, C/C backbone based or protein-ligand 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.