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Updated: Jul 19, 2026
Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
Published on: July 16, 2017
Bhageerath: an energy based web enabled computer software suite for limiting the search space of tertiary structures
B Jayaram1, Kumkum Bhushan, Sandhya R Shenoy
1Department of Chemistry and Supercomputing Facility for Bioinformatics and Computational Biology, Indian Institute of Technology Delhi Hauz Khas, New Delhi 110 016, India. bjayaram@chemistry.iitd.ac.in
Abstract:
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 A 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.
