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Table 3 Function comparison: native recognition

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

  Ranknat RMSDbest Znat CCnat FEnat (%)
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
  1. 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 Ranknat and RMSDbest. Higher ones are better for Znat, CCnat and FEnat. LoCo outperforms all other functions except DFMAC in every measure. All metrics are defined in Performance measures at the end of Methods.