Table 3 Performance of the DFMAC function on the test decoy sets grouped by their generation methods.
From: A knowledge-based structure-discriminating function that requires only main-chain atom coordinates
protein | N | Rnat | C α RMSD | Z-score | C.C. | F.E.(%) | RB1 | logPB1 | RB10 | logPB10 | C.C.decoy | F.E.decoy(%) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
4state_reduced | ||||||||||||
1ctf | 631 | 1 | 0.000 | 4.485 | 0.817 | 68.3 | 61 | -1.01 | 3 | -2.32 | 0.815 | 66.7 |
2cro | 675 | 1 | 0.000 | 3.166 | 0.822 | 53.7 | 7 | -1.98 | 2 | -2.53 | 0.820 | 53.7 |
4rxn | 678 | 1 | 0.000 | 2.895 | 0.670 | 65.7 | 71 | -0.98 | 3 | -2.35 | 0.665 | 64.2 |
Average | 661.3 | 1.0 | 0.000 | 3.515 | 0.770 | 62.6 | 46.3 | -1.33 | 2.7 | -2.40 | 0.767 | 61.5 |
fisa | ||||||||||||
2cro | 501 | 1 | 0.000 | 4.190 | 0.280 | 24.0 | 3 | -2.22 | 2 | -2.40 | 0.253 | 24.0 |
Average | 501.0 | 1.0 | 0.000 | 4.190 | 0.280 | 24.0 | 3.0 | -2.22 | 2.0 | -2.40 | 0.253 | 24.0 |
fisa_casp3 | ||||||||||||
1bl0 | 972 | 8 | 5.522 | 2.174 | 0.302 | 20.6 | 15 | -1.81 | 15 | -1.81 | 0.296 | 19.6 |
l30 | 1401 | 1 | 1.882 | 3.835 | 0.128 | 18.6 | 455 | -0.49 | 3 | -2.67 | 0.111 | 17.9 |
Average | 1186.5 | 4.5 | 3.702 | 3.005 | 0.215 | 19.6 | 235.0 | -1.15 | 9.0 | -2.24 | 0.204 | 18.7 |
hg_structal | ||||||||||||
1bab-B | 30 | 1 | 0.000 | 1.868 | 0.904 | 66.7 | 10 | -0.46 | 2 | -1.16 | 0.892 | 0.0 |
1ecd | 30 | 1 | 0.000 | 1.364 | 0.896 | 100.0 | 2 | -1.16 | 2 | -1.16 | 0.898 | 50.0 |
1gdm | 30 | 1 | 0.000 | 2.395 | 0.880 | 33.3 | 4 | -0.86 | 2 | -1.16 | 0.845 | 0.0 |
1hbh-B | 30 | 1 | 0.000 | 1.205 | 0.893 | 33.3 | 6 | -0.68 | 2 | -1.16 | 0.888 | 0.0 |
1hlb | 30 | 1 | 0.000 | 1.661 | 0.812 | 33.3 | 15 | -0.29 | 2 | -1.16 | 0.812 | 0.0 |
1ith-A | 30 | 1 | 0.000 | 1.775 | 0.904 | 33.3 | 23 | -0.10 | 2 | -1.16 | 0.893 | 0.0 |
1mbs | 30 | 18 | 1.823 | -0.270 | 0.754 | 33.3 | 3 | -0.99 | 2 | -1.16 | 0.835 | 0.0 |
1myt | 30 | 1 | 0.000 | 2.429 | 0.762 | 100.0 | 2 | -1.16 | 2 | -1.16 | 0.725 | 50.0 |
2lhb | 30 | 1 | 0.000 | 1.976 | 0.563 | 33.3 | 12 | -0.38 | 4 | -0.86 | 0.460 | 0.0 |
4sdh-A | 30 | 1 | 0.000 | 3.221 | 0.839 | 33.3 | 21 | -0.14 | 2 | -1.16 | 0.750 | 0.0 |
Average | 30.0 | 2.7 | 0.182 | 1.762 | 0.821 | 50.0 | 9.8 | -0.62 | 2.2 | -1.13 | 0.800 | 10.0 |
ig_structal | ||||||||||||
1bbd | 61 | 1 | 0.000 | 2.304 | 0.605 | 16.7 | 27 | -0.35 | 10 | -0.78 | 0.554 | 0.0 |
1dfb | 61 | 7 | 1.854 | 0.864 | 0.530 | 16.7 | 12 | -0.70 | 4 | -1.18 | 0.528 | 16.7 |
1fai | 61 | 4 | 1.736 | 1.172 | 0.481 | 16.7 | 13 | -0.66 | 4 | -1.18 | 0.462 | 0.0 |
1fig | 61 | 59 | 1.702 | -2.283 | 0.349 | 0.0 | 21 | -0.46 | 6 | -1.00 | 0.504 | 0.0 |
1fpt | 61 | 2 | 1.333 | 1.358 | 0.583 | 33.3 | 8 | -0.88 | 4 | -1.18 | 0.565 | 16.7 |
1fvd | 61 | 1 | 0.000 | 2.112 | 0.606 | 16.7 | 22 | -0.44 | 2 | -1.48 | 0.574 | 0.0 |
1gig | 61 | 1 | 0.000 | 2.787 | 0.547 | 16.7 | 10 | -0.78 | 10 | -0.78 | 0.469 | 0.0 |
1iai | 61 | 1 | 0.000 | 2.103 | 0.644 | 33.3 | 8 | -0.88 | 2 | -1.48 | 0.613 | 16.7 |
1igf | 61 | 2 | 1.774 | 1.353 | 0.607 | 16.7 | 31 | -0.29 | 8 | -0.88 | 0.591 | 0.0 |
1ikf | 61 | 1 | 0.000 | 2.561 | 0.592 | 33.3 | 8 | -0.88 | 3 | -1.30 | 0.540 | 16.7 |
1jhl | 61 | 1 | 0.000 | 1.380 | 0.333 | 16.7 | 41 | -0.17 | 5 | -1.08 | 0.286 | 0.0 |
1mcp | 61 | 1 | 0.000 | 2.143 | 0.623 | 66.7 | 3 | -1.30 | 2 | -1.48 | 0.585 | 50.0 |
1mrd | 61 | 1 | 0.000 | 2.305 | 0.379 | 16.7 | 51 | -0.07 | 7 | -0.93 | 0.264 | 0.0 |
1ngq | 61 | 1 | 0.000 | 2.716 | 0.543 | 33.3 | 2 | -1.48 | 2 | -1.48 | 0.456 | 16.7 |
1opg | 61 | 1 | 0.000 | 2.175 | 0.575 | 33.3 | 44 | -0.14 | 3 | -1.30 | 0.529 | 33.3 |
1tet | 61 | 1 | 0.000 | 2.323 | 0.567 | 33.3 | 4 | -1.18 | 4 | -1.18 | 0.523 | 16.7 |
1vge | 61 | 1 | 0.000 | 2.766 | 0.208 | 16.7 | 45 | -0.13 | 26 | -0.36 | -0.020 | 0.0 |
2fb4 | 61 | 1 | 0.000 | 2.277 | 0.486 | 16.7 | 32 | -0.27 | 13 | -0.66 | 0.422 | 0.0 |
3hfl | 61 | 1 | 0.000 | 2.648 | 0.243 | 33.3 | 29 | -0.32 | 4 | -1.18 | 0.055 | 16.7 |
7fab | 61 | 1 | 0.000 | 2.941 | 0.614 | 50.0 | 6 | -1.00 | 3 | -1.30 | 0.531 | 33.3 |
Average | 61.0 | 4.5 | 0.420 | 1.900 | 0.506 | 25.8 | 20.9 | -0.62 | 6.1 | -1.11 | 0.452 | 11.7 |
ig_structal_hires | ||||||||||||
1fgv | 20 | 1 | 0.000 | 2.310 | 0.724 | 50.0 | 6 | -0.50 | 2 | -0.98 | 0.633 | 0.0 |
1gaf | 20 | 1 | 0.000 | 2.827 | 0.649 | 50.0 | 8 | -0.38 | 2 | -0.98 | 0.493 | 0.0 |
1kem | 20 | 1 | 0.000 | 1.518 | 0.636 | 50.0 | 11 | -0.24 | 3 | -0.80 | 0.567 | 0.0 |
1nbv | 20 | 10 | 1.719 | 0.169 | 0.399 | 0.0 | 7 | -0.43 | 4 | -0.68 | 0.452 | 0.0 |
1vge | 20 | 1 | 0.000 | 2.334 | 0.385 | 50.0 | 15 | -0.10 | 2 | -0.98 | -0.116 | 0.0 |
2fbj | 20 | 1 | 0.000 | 2.532 | 0.725 | 50.0 | 5 | -0.58 | 2 | -0.98 | 0.614 | 0.0 |
8fab | 20 | 1 | 0.000 | 2.487 | 0.295 | 50.0 | 17 | -0.05 | 8 | -0.38 | -0.228 | 0.0 |
Average | 20.0 | 2.3 | 0.246 | 2.025 | 0.545 | 42.9 | 9.9 | -0.33 | 3.3 | -0.82 | 0.345 | 0.0 |
lattice_ssfit | ||||||||||||
1dkt-A | 1995 | 1 | 0.000 | 7.349 | -0.049 | 8.5 | 996 | -0.30 | 242 | -0.92 | -0.087 | 8.0 |
1pgb | 1997 | 1 | 0.000 | 13.649 | 0.138 | 17.1 | 1909 | -0.02 | 60 | -1.52 | 0.087 | 16.6 |
Average | 1996.0 | 1.0 | 0.000 | 10.499 | 0.045 | 12.8 | 1452.5 | -0.16 | 151.0 | -1.22 | 0.000 | 12.3 |
lmds | ||||||||||||
1b0n-B | 498 | 1 | 0.000 | 2.819 | 0.066 | 20.4 | 336 | -0.17 | 10 | -1.70 | 0.038 | 18.4 |
1dtk | 216 | 70 | 7.224 | 0.375 | 0.044 | 4.8 | 42 | -0.71 | 24 | -0.95 | 0.038 | 4.8 |
1shf-A | 437 | 1 | 0.000 | 4.275 | 0.064 | 11.6 | 378 | -0.06 | 2 | -2.34 | -0.004 | 9.3 |
4pti | 344 | 3 | 9.434 | 2.570 | 0.098 | 23.5 | 220 | -0.19 | 4 | -1.93 | 0.063 | 20.6 |
Average | 373.8 | 18.8 | 4.165 | 2.510 | 0.068 | 15.1 | 244.0 | -0.28 | 10.0 | -1.73 | 0.034 | 13.3 |
semfold | ||||||||||||
1eh2 | 11442 | 61 | 12.125 | 2.342 | 0.070 | 13.6 | 6511 | -0.25 | 434 | -1.42 | 0.069 | 13.5 |
1pgb | 11282 | 1 | 0.000 | 7.782 | 0.096 | 19.2 | 2 | -3.75 | 2 | -3.75 | 0.091 | 19.2 |
Average | 11362.0 | 31.0 | 6.063 | 5.062 | 0.083 | 16.4 | 3256.5 | -2.00 | 218.0 | -2.59 | 0.080 | 16.3 |
moulder | ||||||||||||
1c2r | 301 | 1 | 0.000 | 2.803 | 0.774 | 73.3 | 10 | -1.48 | 2 | -2.18 | 0.768 | 70.0 |
1cid | 301 | 1 | 0.000 | 2.759 | 0.753 | 53.3 | 38 | -0.90 | 2 | -2.18 | 0.748 | 53.3 |
1gky | 300 | 1 | 0.000 | 4.713 | 0.828 | 90.0 | 11 | -1.43 | 3 | -2.00 | 0.819 | 89.7 |
1mup | 301 | 1 | 0.000 | 1.993 | 0.847 | 73.3 | 11 | -1.44 | 3 | -2.00 | 0.845 | 73.3 |
2cmd | 301 | 1 | 0.000 | 2.506 | 0.911 | 36.7 | 15 | -1.30 | 6 | -1.70 | 0.911 | 33.3 |
2pna | 301 | 85 | 3.523 | 0.723 | 0.816 | 66.7 | 30 | -1.00 | 4 | -1.88 | 0.817 | 66.7 |
8i1b | 301 | 1 | 0.000 | 2.106 | 0.842 | 46.7 | 16 | -1.27 | 4 | -1.88 | 0.840 | 46.7 |
Average | 300.9 | 13.0 | 0.503 | 2.515 | 0.824 | 62.9 | 18.7 | -1.26 | 3.4 | -1.97 | 0.821 | 61.9 |
rosetta | ||||||||||||
1a68 | 141 | 1 | 0.000 | 2.608 | 0.624 | 64.3 | 11 | -1.11 | 3 | -1.67 | 0.608 | 64.3 |
1aiu | 141 | 15 | 1.385 | 0.805 | 0.777 | 7.1 | 40 | -0.54 | 25 | -0.75 | 0.776 | 7.1 |
1bk2 | 141 | 1 | 0.000 | 2.562 | 0.820 | 78.6 | 14 | -1.00 | 3 | -1.67 | 0.812 | 78.6 |
1bq9 | 141 | 2 | 9.242 | 1.895 | 0.544 | 50.0 | 131 | -0.03 | 2 | -1.85 | 0.532 | 50.0 |
1cc8 | 141 | 1 | 0.000 | 3.317 | 0.848 | 64.3 | 11 | -1.11 | 2 | -1.85 | 0.851 | 57.1 |
1ctf | 141 | 1 | 0.000 | 4.288 | 0.783 | 28.6 | 30 | -0.67 | 6 | -1.37 | 0.780 | 28.6 |
1elw | 141 | 22 | 3.619 | 1.082 | -0.063 | 7.1 | 132 | -0.03 | 12 | -1.07 | -0.070 | 7.1 |
1eyv | 141 | 1 | 0.000 | 3.194 | 0.587 | 35.7 | 22 | -0.80 | 2 | -1.85 | 0.564 | 35.7 |
1gvp | 141 | 1 | 0.000 | 3.018 | 0.540 | 21.4 | 61 | -0.36 | 15 | -0.97 | 0.514 | 21.4 |
1iib | 141 | 1 | 0.000 | 6.093 | 0.595 | 71.4 | 9 | -1.19 | 2 | -1.85 | 0.629 | 71.4 |
1lou | 141 | 1 | 0.000 | 2.664 | 0.741 | 71.4 | 8 | -1.24 | 3 | -1.67 | 0.731 | 64.3 |
1pgx | 141 | 1 | 0.000 | 2.232 | 0.821 | 35.7 | 75 | -0.27 | 5 | -1.45 | 0.820 | 28.6 |
1rnb | 141 | 8 | 13.461 | 1.445 | 0.440 | 21.4 | 89 | -0.20 | 14 | -1.00 | 0.427 | 21.4 |
1ten | 141 | 1 | 0.000 | 4.986 | 0.866 | 92.9 | 5 | -1.45 | 2 | -1.85 | 0.876 | 85.7 |
1tul | 141 | 5 | 0.842 | 2.002 | 0.763 | 64.3 | 16 | -0.94 | 3 | -1.67 | 0.755 | 57.1 |
1urn | 141 | 1 | 0.000 | 2.452 | 0.694 | 64.3 | 9 | -1.19 | 3 | -1.67 | 0.680 | 57.1 |
1vie | 141 | 1 | 0.000 | 3.470 | 0.791 | 71.4 | 2 | -1.85 | 2 | -1.85 | 0.781 | 71.4 |
256b | 141 | 1 | 0.000 | 4.974 | 0.426 | 7.1 | 118 | -0.07 | 42 | -0.52 | 0.390 | 0.0 |
2ci2 | 141 | 80 | 10.219 | 0.075 | -0.020 | 0.0 | 123 | -0.06 | 71 | -0.30 | -0.022 | 0.0 |
Average | 141.0 | 7.6 | 2.040 | 2.798 | 0.609 | 45.1 | 47.7 | -0.74 | 11.4 | -1.41 | 0.602 | 42.5 |