A comparison of heuristic search algorithms for molecular docking. Results indicate that the genetic algorithm obtains the best median energies, although tabu search gives results in closer agreement with crystallographic ligand conformations, indicating the possibility of hybrid seearch mechanisms giving results even better than any of the above. Academic Press, London, 1996. The paper uses the DOCK program to examine possible orientations of a molecule within an active site by superimposition of atoms onto precomputed site locations. A selection of different search methods are compared, such as a matching algorithm based on a single docking graph.
Performance is measured by screening a small database of molecules to a variety of targets.
Results indicate that the site point-directed search is significantly faster than random search, and that the single graph matching algorithm is up to sixty times faster, outperforming the older bipartite graph matching algorithm. This work uses the Dock program to explore the molecular docking issues of sampling and optimization. Molecular Docking Towards Drug Discovery. Jeffery, C.J. and Koshland, Jr., D.E. Three-dimensional structural model of the serine receptor ligand binding domain. A genetic algorithm based method for docking flexible molecules.