Table 1:

Fraction of calculations in which a native binding pose (RMSD from xtal structure < 2 Å) is within a specified cutoff of the minimum-energy structure. Binding poses were obtained either by scoring the crystal structure and docking (xtal + DOCK 6), from BPMF calculations with the Desolvated or Full options at milestone D, or all of the above. Docking poses were the 50 best-scoring poses from docking in which the ligand center of mass is within 6 Å of the center of mass of the crystallographic pose. Scoring was based on one of three force fields: the UCSF DOCK 6 grid score (D6), milestone D, or milestone E. The score was either the minimum or mean interaction energy Ψ, minimum or mean total energy u, or free energy based on reweighing the interaction energy (Equation 13 and 14) or total energy (Equation 12 and 14). Parentheses contain the standard error of the sample proportion, $\sqrt{p\left(1-p\right)/n}$.

Samples	Scoring		Native within energy of minimum (kBT)
	Force Field	Score Type	8	4	2	0
xtal + DOCK 6	D6	min Ψ	0.941 (0.026)	0.906 (0.032)	0.847 (0.039)	0.812 (0.042)
	E	min u	0.953 (0.023)	0.953 (0.023)	0.929 (0.028)	0.929 (0.028)
	E	min Ψ	0.953 (0.023)	0.918 (0.030)	0.882 (0.035)	0.871 (0.036)
Desolvated	D	min u	0.845 (0.012)	0.781 (0.014)	0.732 (0.014)	0.682 (0.015)
	D	mean u	0.847 (0.012)	0.769 (0.014)	0.705 (0.015)	0.653 (0.016)
	D	fe u	0.919 (0.009)	0.912 (0.009)	0.873 (0.011)	0.690 (0.015)
	D	min Psi	0.886 (0.010)	0.826 (0.012)	0.786 (0.013)	0.716 (0.015)
	D	mean Psi	0.890 (0.010)	0.842 (0.012)	0.803 (0.013)	0.714 (0.015)
	D	fe Psi	0.919 (0.009)	0.912 (0.009)	0.873 (0.011)	0.690 (0.015)
	E	min u	0.833 (0.012)	0.811 (0.013)	0.788 (0.013)	0.771 (0.014)
	E	mean u	0.830 (0.012)	0.796 (0.013)	0.772 (0.014)	0.752 (0.014)
	E	fe u	0.842 (0.012)	0.813 (0.013)	0.787 (0.013)	0.758 (0.014)
	E	min Psi	0.848 (0.012)	0.831 (0.012)	0.814 (0.013)	0.788 (0.013)
	E	mean Psi	0.842 (0.012)	0.818 (0.013)	0.788 (0.013)	0.757 (0.014)
	E	fe Psi	0.856 (0.011)	0.818 (0.013)	0.799 (0.013)	0.767 (0.014)
Full	D	min u	0.883 (0.010)	0.804 (0.013)	0.753 (0.014)	0.699 (0.015)
	D	mean u	0.905 (0.010)	0.825 (0.012)	0.759 (0.014)	0.682 (0.015)
	D	fe u	0.948 (0.007)	0.943 (0.008)	0.899 (0.010)	0.702 (0.015)
	D	min Psi	0.910 (0.009)	0.867 (0.011)	0.816 (0.013)	0.741 (0.014)
	D	mean Psi	0.921 (0.009)	0.872 (0.011)	0.831 (0.012)	0.734 (0.014)
	D	fe Psi	0.948 (0.007)	0.943 (0.008)	0.899 (0.010)	0.702 (0.015)
	E	min u	0.897 (0.010)	0.866 (0.011)	0.843 (0.012)	0.820 (0.013)
	E	mean u	0.893 (0.010)	0.863 (0.011)	0.839 (0.012)	0.807 (0.013)
	E	fe u	0.908 (0.009)	0.879 (0.011)	0.864 (0.011)	0.839 (0.012)
	E	min Psi	0.910 (0.009)	0.893 (0.010)	0.876 (0.011)	0.846 (0.012)
	E	mean Psi	0.897 (0.010)	0.880 (0.011)	0.864 (0.011)	0.834 (0.012)
	E	fe Psi	0.913 (0.009)	0.884 (0.010)	0.868 (0.011)	0.840 (0.012)
All	E	min u	0.918 (0.030)	0.906 (0.032)	0.882 (0.035)	0.882 (0.035)
	E	min Ψ	0.941 (0.026)	0.918 (0.030)	0.894 (0.033)	0.871 (0.036)