Abstract
AEDock based on AutoDock2.4 is developed with annealing evolution algorithm (AEA) in place of simulated annealing algorithm (SA) for supermolecular conformation searching. Because AEA takes advantage of both the genetic algorithm (GA) and the simulated annealing algorithm, the results of AEDock show that AEA can predict the binding conformations of ligands with up to 10 rotatable bonds to a rigid macromolecular target. The case of 1 hvr is only one of six cases where SA in AutoDock 2.4 failed to find an energy less than that of the crystal. It is used here to compare the performance of SA with AEA. The results of comparison show that fewer states are needed in AEA than in SA, but the success rate of AEA is much higher.
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