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 (Morris et
al. 1996), a physical model is used to evaluate the energy of
candidate docked configurations, 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 finding the true
physical docked configuration.  We use these results to test the
energy function and evaluate the success of the application.