A parallel Monte Carlo search algorithm for the conformational analysis of proteins

Authors:
Daniel R. Ripoll;Stephen J. Thomas
Affiliations:
National Research Council of Canada, Biotechnology Research Institute, 6100 Rayalmount Ave., Montréal, Quebec, H4P 2R2, Canada;National Research Council of Canada, Biotechnology Research Institute, 6100 Rayalmount Ave., Montréal, Quebec, H4P 2R2, Canada
Venue:
Proceedings of the 1990 ACM/IEEE conference on Supercomputing
Year:
1990

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Abstract

In recent years several approaches have been proposed to overcome the multiple minima problem associated with non-linear optimization techniques used in the analysis of molecular conformations. One such technique based on a parallel Monte Carlo search algorithm is analysed. 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.