Table 2.

Correlation coefficients between predicted and experimental ligand binding affinities for subsets of BACE-1 ligands modeled in different protein conformations. R² is Pearson’s r squared. The standard deviations do not account for the experimental uncertainty. 4EWO, 2WF3, 2B8V, and 2P4J are the PDB codes of the different protein conformations used. n refers to the total number of ligands in each dataset. For MM-GBSA scores, affinities of ligands modeled in 4EWO have the weakest correlation with the experimental affinities. For AutoDock4, affinities of ligands modeled in different protein conformations have similar correlation coefficients with the experimental values.

	4EWO (n=75)
	Kendall’s τ	Pearson’s r	Spearman’s ρ	R2
AutoDock4	0.26 ± 0.09	0.32 ± 0.14	0.36 ± 0.12	0.10 ± 0.09
MM-GBSA	0.15 ± 0.09	0.27 ± 0.12	0.22 ± 0.12	0.08 ± 0.06
	2WF3 (n=69), 2B8V (n=5) or 2P4J (n=5)
	Kendall’s τ	Pearson’s r	Spearman’s ρ	R2
AutoDock4	0.23 ± 0.09	0.33 ± 0.12	0.29 ± 0.12	0.11 ± 0.07
MM-GBSA	0.36 ± 0.07	0.53 ± 0.09	0.50 ± 0.09	0.28 ± 0.09