Automated docking of peptides and proteins by genetic algorithm

Genetic algorithm (GA) combined with random search has been applied to thoroughly search the appropriate associated sites for both peptide and protein complexes. Steric complementarity and energetic complementarity of ligand with its receptor have been separately considered in our two-stage automated docking. Eight complexes have been randomly selected from the Protein Data Bank to test our procedure. Conformations and orientations close to the crystallographically determined structures are obtained. For most cases, the smallest RMS (root mean square of distance) of the GA solutions is smaller than 1.0.