IMPLEMENTATION OF THE ECEPP ALGORITHM, THE MONTE-CARLO MINIMIZATION METHOD, AND THE ELECTROSTATICALLY DRIVEN MONTE-CARLO METHOD ON THE KENDALL SQUARE RESEARCH KSR1 COMPUTER

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 electrostatica lly driven Monte Carlo (EDMC) method] to the Kendall Square Research K SR1 computer is described. The MCM and EDMC methods were developed to surmount the multiple-minima problem in protein folding. Parallelizati on of these codes led to substantial speedups (expressed as the ratio between the mean time per energy evaluation in one processor and the m ean time per energy evaluation in a set of processors) over the serial versions of these codes. A comparison of the performance of these alg orithms on the KSR1 and on the IBM ES9000 computers is presented. (C) 1995 by John Wiley & Sons, Inc.