Table 1.

Comparing binding free energies for 24 ligands obtained using YANK and FFTΔG. The FFT-based free energies were calculated using different weighting schemes, as defined in the main text. RMSE is in units of kcal/mol.

	Full (24)			Active (11)		Inactive (13)
Weighting scheme	Linear regression	RMSE	R	RMSE	R	RMSE	R
a	y = 1.12x + 2.28	2.31(0.28)	0.90(0.06)	2.35(0.57)	0.59(0.21)	2.28(0.24)	0.96(0.02)
b	y = 1.19x + 2.32	2.23(0.31)	0.90(0.06)	2.09(0.54)	0.58(0.18)	2.34(0.26)	0.96(0.02)
c	y = 1.17x + 2.25	2.17(0.28)	0.91(0.05)	2.09(0.59)	0.62(0.13)	2.24(0.26)	0.96(0.02)
d	y = 1.22x + 2.11	2.07(0.29)	0.90(0.06)	1.86(0.60)	0.59(0.13)	2.24(0.28)	0.96(0.03)
e	y = 1.24x + 1.90	2.28(0.37)	0.87(0.07)	1.99(0.84)	0.38(0.23)	2.50(0.30)	0.94(0.03)
f	y = 1.19x + 2.01	2.25(0.32)	0.88(0.07)	2.08(0.74)	0.41(0.19)	2.39(0.27)	0.94(0.03)