The Lamarckian Genetic Algorithm was used to perform the dockings and all remaining parameters were set to their default values. The center of the cubic search space with an edge length of 20 Å was defined as the center of mass of the ligand. The five complexes with reactive Asp and Glu side chains of the CSKDE95 benchmark could not be docked with AutoDock4, as these residues are not implemented in the alignment procedure of ADT.