Table 1.

Effects of nonpolar solvent modeling (inp) upon the performance of MMPBSA to predict relative binding affinities. All calculations were conducted with the default SES surface (sasopt=0), the default solvent probe (dprob=1.4), the default atomic radius option (radiopt=0), and the default grid spacing of 0.50 Angstrom (space=0.50). The RMSD’s of ΔΔG are in kcal/mol.

Systems	INP=1			INP=2
	RMSD	R	Slope	RMSD	R	Slope
CDK+PKA	5.81	0.81	0.18	3.42	0.71	0.29
glucosidase	4.43	0.57	0.16	1.94	0.30	0.23
thrombin	11.02	0.87	0.23	4.26	0.86	0.42
trypsin	9.89	0.74	0.18	3.30	0.53	0.32
urokinase	7.19	0.73	0.22	2.61	0.53	0.33
Factor Xa	5.99	0.75	0.23	3.26	0.67	0.27