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

BMC Bioinformatics

Table 3 Function comparison: native recognition

	Rank_nat	RMSD_best	Z_nat	CC_nat	FE_nat (%)
LoCo	13.4	1.62	1.805	0.519	36.6
DFMAC	6.7	1.17	2.630	0.562	38.3
RF_CB_SRS_OD	19.3	2.68	1.508	0.464	31.3
ProSa 2003	44.0	2.39	1.288	0.491	33.8
Four-body	81.8	4.87	0.621	0.334	20.4
General-four-body	56.3	4.67	0.797	0.311	18.9
Short-range	87.5	4.87	0.353	0.257	13.0
BFKV	54.5	3.54	0.774	0.397	24.7
BT	45.8	3.85	0.744	0.390	23.2
GKS	28.5	5.42	0.229	0.235	12.3
HLPL	31.4	3.37	0.602	0.383	24.8
MJ1	124.5	3.79	0.014	0.336	20.4
MJ2h	101.3	3.20	0.324	0.377	23.0
MJ3	50.6	4.69	0.401	0.244	15.7
MJ3h	52.1	3.63	0.733	0.410	26.3
MJPL	57.8	3.33	0.246	0.353	23.0
MS	54.0	4.94	0.419	0.234	13.3
MSBM	54.2	5.77	0.119	0.159	7.5
Qa	37.4	4.72	0.749	0.296	20.4
Qm	31.6	4.35	0.723	0.275	19.2
Qp	28.8	3.12	0.513	0.365	24.3
RO	248.3	5.67	0.287	0.248	17.6
SKJG	34.1	4.16	0.756	0.369	21.4
SKOa	33.1	4.35	0.664	0.352	20.5
SKOb	30.3	4.11	0.652	0.363	21.8
TD	47.7	3.81	0.739	0.399	24.2
Tel	80.0	4.03	0.740	0.370	23.5
TEs	54.2	4.50	0.646	0.331	17.2
TS	66.1	3.13	0.234	0.355	24.3
VD	73.7	5.09	0.478	0.290	17.5

Native structure recognition performance comparison among scoring functions. 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. LoCo outperforms all other functions except DFMAC in every measure. All metrics are defined in Performance measures at the end of Methods.

ISSN: 1471-2105