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A parallel Monte Carlo search algorithm for the conformational analysis of polypeptides |
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| Authors: | Daniel R Ripoll Stephen J Thomas |
| Affiliation: | (1) Molecular Biology, Biotechnology Research Institute, National Research Council of Canada, 6100 Royalmount Avenue, H4P 2R2 Montréal, Québec, Canada;(2) Present address: Département d'informatique et de recherche opérationelle, Université de Montréal, Succ.  A , Case Postale 6128, H3C 3J7 Montréal, Québec, Canada |
| Abstract: | In recent years several approaches have been proposed to overcome the multiple-minima problem associated with nonlinear optimization techniques used in the analysis of molecular conformations. One such technique based on a parallel Monte Carlo search algorithm is analyzed. Experiments on the Intel iPSC/2 confirm that the attainable parallelism is limited by the underlying acceptance rate in the Monte Carlo search. It is proposed that optimal performance can be achieved in combination with vector processing. Tests on both the IBM 3090 and Intel iPSC/2-VX indicate that vector performance is related to molecule size and vector pipeline latency. |
| Keywords: | Monte Carlo structure analysis polypeptides vector processing supercomputer |
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