Table I.

Correlation Coefficients (R) between MM-GBSA or MM-PBSA Calculations and Experimental Binding Free Energies for Dielectric Constant ε=1.0 or 4.0.

Protein Targets (# of Ligands)	MM-GBSA (ε=4.0)	MM-GBSA (ε=1.0)	MM-PBSA (ε=4.0)	MM-PBSA (ε=1.0)
trypsin β (57)	0.72	0.58	0.70	0.40
thrombin α (28)	0.73	0.63	0.74	0.42
CDK+PKA (19)	0.77	0.58	0.78	0.62
urokinase-type plasminogen activator (19)	0.79	0.75	0.78	0.68
β-glucosidase A (18)	0.61	0.18	0.56	0.16
coagulation factor Xa (15)	0.67	0.58	0.67	0.45