Table 3. Comparing different free energy estimates with experiment.

AlGDock calculations were based on 384 snapshots from simulations with active ligands, weighted according to scheme (c). As DOCK 6 does not have an implicit solvent, OBC2 and PBSA describe the receptor potential energies used for snapshot weights. The outlier iodobenzene is excluded from this analysis. For the same table including the outlier, see Table S7 of the SI.

Method	Implicit solvent	Spearman ρ	Kendall τ	Pearson R	RMSE
DOCK 6	OBC2	0.36(0.00)	0.24(0.01)	0.45(0.04)	12.06(0.37)
DOCK 6	PBSA	0.44(0.00)	0.33(0.01)	0.50(0.04)	12.62(0.36)
min Ψ	OBC2	0.39(0.01)	0.27(0.02)	0.55(0.04)	15.46(0.57)
min Ψ	PBSA	0.45(0.01)	0.35(0.01)	0.56(0.03)	14.03(0.59)
mean Ψ	OBC2	0.39(0.01)	0.29(0.01)	0.51(0.04)	9.64(0.47)
mean Ψ	PBSA	0.56(0.00)	0.44(0.01)	0.60(0.05)	7.50(0.38)
MBAR-based	OBC2	0.34(0.01)	0.23(0.02)	0.44(0.06)	1.60(0.17)
MBAR-based	PBSA	0.62(0.01)	0.48(0.01)	0.65(0.05)	2.81(0.32)