Bhageerath: an energy based web enabled computer software suite for limiting the search space of tertiary structures of small globular proteins.
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.
Jayaram
B
B
Department 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
Bhushan
Kumkum
K
Shenoy
Sandhya R
SR
Narang
Pooja
P
Bose
Surojit
S
Agrawal
Praveen
P
Sahu
Debashish
D
Pandey
Vidhu
V
D019295:Computational Biology; D020407:Internet; D017510:Protein Folding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry; D020539:Sequence Analysis, Protein; D012984:Software
D011506:Proteins