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

✍ Scribed by Jin, A. Y.; Leung, F. Y.; Weaver, D. F.

• Publisher: John Wiley and Sons
• Year: 1999
• Tongue: English
• Weight: 279 KB
• Volume: 20
• Category: Article
• ISSN: 0192-8651
• DOI: 10.1002/(sici)1096-987x(199910)20:13<1329::aid-jcc1>3.0.co;2-h

✦ Synopsis

Three genetic algorithm programs, GAP 1.0, 2.0, and 3.0, were used in conjunction with the ECEPPr2 force field to search the conformation w x 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 -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.