Flexible ligand docking using a genetic algorithm.
Two computational techniques have been developed to explore the orientational and conformational space of a flexible ligand within an enzyme. Both methods use the Genetic Algorithm (GA) to generate conformationally flexible ligands in conjunction with algorithms from the DOCK suite of programs to characterize the receptor site. The methods are applied to three enzyme-ligand complexes: dihydrofolate reductase-methotrexate, thymidylate synthase-phenolpthalein and HIV protease-thioketal haloperidol. Conformations and orientations close to the crystallographically determined structures are obtained, as well as alternative structures with low energy. The potential for the GA method to screen a database of compounds is also examined. A collection of ligands is evaluated simultaneously, rather than docking the ligands individually into the enzyme.
Oshiro
C M
CM
Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco 94143-0446, USA.
Kuntz
I D
ID
Dixon
J S
JS
D000465:Algorithms; D018360:Crystallography, X-Ray; D004798:Enzymes / Q000737:chemistry* / Q000378:metabolism; D016333:HIV Protease / Q000737:chemistry / Q000378:metabolism; D006220:Haloperidol / Q000031:analogs & derivatives / Q000737:chemistry / Q000378:metabolism; D008024:Ligands; D008727:Methotrexate / Q000737:chemistry / Q000378:metabolism; D008957:Models, Genetic; D008958:Models, Molecular; D008968:Molecular Conformation; D020113:Phenolphthalein; D010635:Phenolphthaleins / Q000737:chemistry / Q000378:metabolism; D011487:Protein Conformation; D013762:Tetrahydrofolate Dehydrogenase / Q000737:chemistry / Q000378:metabolism; D013940:Thymidylate Synthase / Q000737:chemistry / Q000378:metabolism
D004798:Enzymes; D008024:Ligands; D010635:Phenolphthaleins; C094606:thioketal haloperidol; D020113:Phenolphthalein; D013762:Tetrahydrofolate Dehydrogenase; D013940:Thymidylate Synthase; D016333:HIV Protease; D006220:Haloperidol; D008727:Methotrexate