Three variations of genetic algorithm for searching biomolecular conformation space: Comparison of GAP 1.0, 2.0, and 3.0

Three genetic algorithm programs, GAP 1.0, 2.0, and 3.0, were used in conjunction with the ECEPP/2 force field to search the conformation space of [Met]-enkephalin. Each program was proficient at quickly finding many diverse low-energy conformers. Conformer populations displayed a variety of secondary structure motifs including those likely to bind to the mu-opioid receptor. Limitations in the program's sampling behavior are discussed and method improvements are suggested. Although still in a developmental stage, the GAP programs represent a useful addition to conformational search techniques when no a priori structural information is available. (C) 1999 John Wiley & Sons, Inc.