title: A family competition evolutionary algorithm for automated docking of flexible ligands to proteins.
abstract: In this paper, we study an evolutionary algorithm for flexible ligand docking. Based on family competition and adaptive rules, the proposed approach consists of global and local strategies by integrating decreasing mutations and self-adaptive mutations. To demonstrate the robustness of the proposed approach, we apply it to the problems of the first international contests on evolutionary optimization. Following the description of function optimization, our approach is applied to a dihydrofolate reductase enzyme with the anti-cancer drug methotrexate and with two analogs of the antibacterial drug trimethoprim. Our numerical results indicate that the proposed approach is robust. The docked lowest energy structures have rms derivations ranging from 0.72 A to 1.98 A with respect to the corresponding crystal structure.
authors.affiliation: Department of Computer Science and Information Engineering, National Taiwan University, Taipei.
authors.forename: J M
authors.initials: JM
authors.lastname: Yang
authors.forename: C Y
authors.initials: CY
authors.lastname: Kao
mesh_terms: D000465:Algorithms; D005075:Biological Evolution; D008024:Ligands; D008727:Methotrexate / Q000737:chemistry / Q000378:metabolism; D008958:Models, Molecular; D009154:Mutation; D011485:Protein Binding; D011506:Proteins / Q000235:genetics / Q000378:metabolism; D013762:Tetrahydrofolate Dehydrogenase / Q000737:chemistry / Q000235:genetics / Q000378:metabolism
chemical_list: D008024:Ligands; D011506:Proteins; D013762:Tetrahydrofolate Dehydrogenase; D008727:Methotrexate