Conformational space annealing by parallel computations: Extensive conformational search of Met-enkephalin and of the 20-residue membrane-bound portion of melittin

✍ Scribed by Jooyoung Lee; Harold A. Scheraga

• Publisher: John Wiley and Sons
• Year: 1999
• Tongue: English
• Weight: 286 KB
• Volume: 75
• Category: Article
• ISSN: 0020-7608
• DOI: 10.1002/(sici)1097-461x(1999)75:3<255::aid-qua15>3.0.co;2-v

✦ Synopsis

A successful implementation of a parallel version of a conformational Ž . space annealing CSA method is presented. The CSA method, an optimization procedure for conformational energy calculations on polypeptides, searches the whole conformational space in its early stages and then narrows the search to smaller regions with low energy and distinct geometry. By selecting 20 seed conformations that are far from each other in the conformational space, the CSA method generates up to 400 conformations to be minimized independently, thereby allowing very efficient parallel computations to be carried out. When applied to the pentapeptide Met-enkephalin, the Ž . Ž global minimum-energy conformation GMEC of the ECEPPr3 Empirical . Conformational Energy Program for Peptides force field was found for all of 600 separate runs after about 35.5 s each, on average, of wall clock time, using 16 processors of an IBM SP2 supercomputer. The GMEC of the 20-residue membrane-bound portion of melittin was also found for all of 24 independent runs. The average wall clock time to find the GMEC of this 20-residue peptide, using 32 processors of an IBM SP2 supercomputer, was about 4.5 h per run.