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Nucleic Acids Research Advance Access published online on November 7, 2006
Nucleic Acids Research, doi:10.1093/nar/gkl789
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© 2006 The Author(s).
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Computational Biology

Bhageerath: an energy based web enabled computer software suite for limiting the search space of tertiary structures of small globular proteins

B. Jayaram*, Kumkum Bhushan, Sandhya R. Shenoy, Pooja Narang, Surojit Bose, Praveen Agrawal, Debashish Sahu and Vidhu Pandey

Department of Chemistry and Supercomputing Facility for Bioinformatics and Computational Biology, Indian Institute of Technology Delhi Hauz Khas, New Delhi 110 016, India

*To whom correspondence should be addressed. Tel: +91 11 2659 1505; Fax: +91 11 2658 2037; Email: bjayaram{at}chemistry.iitd.ac.in

Received April 5, 2006. Revised September 27, 2006. Accepted October 2, 2006.

We describe here an energy based computer software suite for narrowing down the search space of tertiary structures of small globular proteins. The protocol comprises eight different computational modules that form an automated pipeline. It combines physics based potentials with biophysical filters to arrive at 10 plausible candidate structures starting from sequence and secondary structure information. The methodology has been validated here on 50 small globular proteins consisting of 2–3 helices and strands with known tertiary structures. For each of these proteins, a structure within 3–6 Å RMSD (root mean square deviation) of the native has been obtained in the 10 lowest energy structures. The protocol has been web enabled and is accessible at http://www.scfbio-iitd.res.in/bhageerath.


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