A Comparison of Global and Local Search Methods in Drug Docking

Molecular docking software makes computational predictions of the interaction of molecules. This can be useful, for example, in evaluating the binding of candidate drug molecules to a target molecule from a virus. In the Autodock docking software 11], a physical model is used to evaluate the energy of candidate docked con gurations, and heuristic search is used to minimize this energy. Previous versions of Autodock used simulated annealing to do this heuristic search. We evaluate the use of the genetic algorithm with local search in Autodock. We investigate several GA-local search (GA-LS) hybrids and compare results with those obtained from simulated annealing. This comparison is done in terms of optimization success, and absolute success in nding the true physical docked con guration. We use these results to test the energy function and evaluate the success of the application. 1 The Docking Problem When two molecules are in close proximity, it can be energetically favorable for them ...

• Type: Conference
• Year: 1997
• Where: ICGA
• Authors: Christopher D. Rosin, R. Scott Halliday, William E. Hart, Richard K. Belew
• Keywords: Docking Software, HIV Protease, ICGA 1997, Molecular Docking, Optimization