Implementation of the ECEPP algorithm, the Monte Carlo minimization method, and the electrostatically driven Monte Carlo method on the Kendall square research KSR1 computer

Abstract

Abstract In this article the adaptation of the Empirical Conformational Energy Program for Peptides (ECEPP/3) and two conformational search methods [viz., the Monte Carlo minimization (MCM) method and the electrostatically driven Monte Carlo (EDMC) method] to the Kendall Square Research KSR1 computer is described. The MCM and EDMC methods were developed to surmount the multiple‐minima problem in protein folding. Parallelization of these codes led to substantial speedups (expressed as the ratio between the mean time per energy evaluation in one processor and the mean time per energy evaluation in a set of processors) over the serial versions of these codes. A comparison of the performance of these algorithms on the KSR1 and on the IBM ES9000 computers is presented. © 1995 by John Wiley & Sons, Inc.