A Comparison of Global and Local Search Methods in Drug Docking

Molecular docking software makes compu tational 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 a phys ical model is used to evaluate the energy of candidate docked con gurations and heuristic search is used to minimize this energy Pre vious versions of Autodock used simulated an nealing to do this heuristic search We eval uate the use of the genetic algorithm with lo cal search in Autodock We investigate several GA local search GA LS hybrids and compare results with those obtained from simulated an nealing 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

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