LoCo: a novel main chain scoring function for protein structure prediction based on local coordinates

BMC Bioinformatics

Table 9 Omega angles and native recognition

	Rank_nat	RMSD_best	Z_nat	CC_nat	FE_nat (%)
LoCo	13.4	1.62	1.805	0.519	36.6
OMEGAS ONLY	12.1	2.40	5.640	0.198	18.6
DFMAC WITH OMEGAS	6.7	1.17	2.630	0.562	38.3
DFMAC WITHOUT OMEGAS	11.9	1.04	2.582	0.558	39.0

Native recognition performance comparison among LoCo, our ω-only function and DFMAC both with and without its ω component is shown. All reported measures are averages over the 77 decoy sets in the final testing group. Lower scores are better for Rank_nat and RMSD_best. Higher ones are better for Z_nat, CC_nat and FE_nat. The ω-only function is able to pick out native structures quite well, but when it fails, its choices are essentially random. In the two measures for which the ω-only function does poorly (CC_nat and FE_nat), DFMAC performance improves when its ω component is removed. All metrics are defined in Performance measures at the end of Methods.

ISSN: 1471-2105