Automated docking of peptides and proteins by genetic algorithm

Genetic algorithm (GA) combined with random search has been applied to thor oughly 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 automate d docking. Eight complexes have been randomly selected from the Protein Dat a Bank to test our procedure. Conformations and orientations close to the c rystallographically determined structures are obtained. For most cases, the smallest RMS (root mean square of distance) of the GA solutions is smaller than 1.0. (C) 1999 Elsevier Science B.V. All rights reserved.