BHAGEERATH: An Energy Based Protein Structure Prediction Server

Bhageerath is 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 5 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.

Bhageerath On Blue Gene

Bhageerath, the protein structure prediction software developed indigenously in-house at IIT Delhi could run on a 1024 processor IBM Blue Gene. Blue Gene is an IBM research project dedicated to exploring the frontiers in supercomputing in terms of computer architecture, software required to program and control the massively parallel systems and in the use of computation to advance the studies of important biological processes such as protein folding. IBM conducted a workshop from 10 - 12 April 2006 in Bangalore, where selected students and scientists from premier institutes like IIT's, IISc's, CDAC were invited to run and test various scientific programs from different areas on the Blue Gene. This gave us an opportunity to remotely test Bhageerath on a 1024 processor Blue Gene machine located in Rochester, USA. It showed significant improvement in speed and showed good scalability. A three helical system which took around 5-6 hours on a 32 processor cluster now took just 726 second (~12 minute) on a 1024 processor Blue Gene machine. We were able to produce following results.

No of Processors Time
1407 sec
726 sec

We would like to thank IBM for giving us this opportunity to test our program on Blue Gene .



[1] Jayaram, B., Bhushan, K., Shenoy, S. R., Narang, P., Bose, S., Agrawal, P., Sahu, D., Pandey, V.S. Bhageerath : An Energy Based Web Enabled Computer Software Suite for Limiting the Search Space of Tertiary Structures of Small Globular Proteins. Nucl Acids Res., 2006, 34, 6195-6204; doi: 10.1093/nar/gkl789 [Full Paper].[FULL PAPER]
[2] Narang, P., Bhushan, K., Bose, S. and Jayaram, B. A computational pathway for bracketing native-like structures for small alpha helical globular proteins. Phys. Chem. Chem. Phys. 2005, 7, 2364-2375.[ FULL PAPER ].
[3] Narang, P., Bhushan, K., Bose, S., and Jayaram, B. Protein structure evaluation using an all-atom energy based empirical scoring function. J. Biomol. Str. Dyn. 2006, 23, 385-406. [ ABSTRACT ].