Flexible ligand docking using a genetic algorithm
- Cite this article as:
- Oshiro, C.M., Kuntz, I.D. & Dixon, J.S. J Computer-Aided Mol Des (1995) 9: 113. doi:10.1007/BF00124402
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.
KeywordsGenetic algorithm DOCK Flexible conformational search Protein-ligand interactions Dihydrofolate reductase Thymidylate synthase HIV protease
genetic algorithm; dhfr, dihydrofolate reductase
human immune deficiency virus