Table 1.

Percent PSSM recovery and percent sequence recovery by degree of burial for 100 proteins used in optimization. “Standard” refers to the standard energy function, “Reference” refers to the modified standard energy function in which the reference energies were reoptimized, and “NV environment KBP” refers to the optimized energy function incorporating the NV environment energy term.

	Percent PSSM Recovery			Percent Sequence Recovery
	Standard	Reference	NV environment KBP	Standard	Reference	NV environment KBP
Buried	73.4%	77.1%	78.9%	64.9%	66.5%	65.5%
Boundary	72.1%	75.3%	77.3%	44.3%	46.6%	45.5%
Surface	70.4%	74.4%	75.9%	32.8%	35.9%	35.5%
Overall	72.0%	75.6%	77.2%	45.7%	48.1%	47.3%