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Table 4 Function comparison: decoy discrimination

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

  RB1 RB10 RMSDdecoy Zdecoy CCdecoy FEdecoy (%) log(PB1) log(PB10)
LoCo 154.8 5.6 3.51 0.938 0.505 31.4 -0.864 -1.640
DFMAC 108.9 13.8 3.64 1.024 0.533 31.6 -0.825 -1.586
RF_CB_SRS_OD 172.8 52.5 4.11 0.914 0.457 28.4 -0.761 -1.524
ProSa 2003 118.2 24.8 3.82 0.931 0.493 32.3 -0.755 -1.650
Four-body 124.8 36.8 5.01 0.539 0.328 19.6 -0.488 -1.317
General-four-body 186.3 52.2 4.97 0.436 0.312 17.1 -0.482 -1.241
Short-range 192.4 36.6 5.27 0.377 0.267 14.9 -0.536 -1.249
BFKV 139.4 32.3 3.98 0.673 0.398 25.3 -0.671 -1.412
BT 175.4 39.0 4.32 0.636 0.391 24.3 -0.558 -1.406
GKS 164.6 71.3 5.57 0.187 0.231 13.0 -0.400 -1.166
HLPL 161.3 31.7 3.86 0.725 0.396 27.3 -0.650 -1.434
MJ1 183.1 34.9 4.54 0.596 0.336 22.5 -0.594 -1.302
MJ2h 149.5 28.4 3.93 0.695 0.407 25.1 -0.640 -1.361
MJ3 172.4 25.3 4.92 0.270 0.241 15.8 -0.476 -1.241
MJ3h 152.2 26.5 4.00 0.641 0.416 25.7 -0.615 -1.417
MJPL 129.5 29.0 4.15 0.693 0.375 25.6 -0.650 -1.363
MS 191.1 67.1 5.09 0.217 0.236 13.4 -0.496 -1.155
MSBM 140.1 65.4 5.77 -0.001 0.165 7.6 -0.359 -1.043
Qa 176.9 32.0 5.02 0.357 0.286 17.2 -0.480 -1.323
Qm 189.6 53.8 5.02 0.356 0.268 16.9 -0.479 -1.224
Qp 163.9 31.4 3.81 0.721 0.377 25.0 -0.622 -1.381
RO 231.3 44.3 5.83 0.197 0.240 15.5 -0.396 -1.194
SKJG 146.4 41.1 4.45 0.504 0.362 20.4 -0.586 -1.309
SKOa 90.7 37.1 4.46 0.469 0.352 20.8 -0.593 -1.328
SKOb 144.3 27.9 4.34 0.573 0.363 21.8 -0.587 -1.395
TD 156.4 30.6 4.17 0.724 0.416 26.3 -0.604 -1.418
Tel 141.3 64.4 4.26 0.540 0.363 22.0 -0.569 -1.402
TEs 163.3 62.1 4.74 0.523 0.338 18.5 -0.522 -1.237
TS 125.5 28.7 4.04 0.697 0.381 26.3 -0.656 -1.358
VD 149.8 48.4 5.22 0.504 0.292 17.3 -0.435 -1.284
  1. Comparison of decoy discrimination performance among all tested functions is shown. All reported measures are averages over the 77 decoy sets in the final testing group. Lower scores are better for RB1, RB10, RMSDdecoy, log(PB1) and log(PB10). Higher scores are better for Zdecoy, CCdecoy and FEdecoy. LoCo outperforms all other functions in RB10, RMSDdecoy, and log(PB1). It is slightly higher than ProSa 2003 in log(PB10) and slightly lower than ProSa 2003 in FEdecoy. Zdecoy, CCdecoy and FEdecoy for LoCo are all slightly lower than for DFMAC. LoCo outperforms the remaining 27 functions in every measure except RB1. All metrics are defined in Performance measures at the end of Methods.