Simulation parameters and results.

AUC averages were calculated without the outlier ATCase. Ligand names are taken from the PDB files. Italicized PDB codes indicate the pair of structures used to calculate RMSD and difference vector. The column labeled “# sim” indicates the total number of simulations performed. “Probed sites” indicates how many of the binding sites our probe managed to reproduce. The AUC values are averages over two independent runs with different random number seeds. The differences between the total averages (bottom row) of the two runs were in the range 0.005–0.015.