Table 2 Performance of the density score function on 83 decoy sets grouped by their generation methods.
From: Improved protein structure selection using decoy-dependent discriminatory functions
Protein (PDB code) | N | RMSD range (Å) | RB 1 | log PB 1 | log PB 10 | F.E.(%) | C.C. | R.C. | R exp | C.C. orig |
|---|---|---|---|---|---|---|---|---|---|---|
4state_reduced | ||||||||||
1ctf | 630 | 1.32 – 9.07 | 7 | -1.95 | -2.8 | 88.9 | 0.98 | 0.99 | 1 | 0.95 |
1r69 | 675 | 0.88 – 8.31 | 7 | -1.98 | -2.83 | 87.4 | 0.96 | 0.98 | 1 | 0.88 |
1sn3 | 660 | 1.31 – 9.13 | 11 | -1.78 | -2.82 | 86.4 | 0.96 | 0.97 | 1 | 0.95 |
2cro | 674 | 0.81 – 8.31 | 1 | -2.82 | -2.83 | 84.6 | 0.96 | 0.98 | 1 | 0.82 |
3icb | 653 | 0.95 – 9.39 | 2 | -2.51 | -2.81 | 84.2 | 0.98 | 0.99 | 4 | 0.95 |
4pti | 687 | 1.41 – 9.27 | 11 | -1.8 | -2.84 | 91.7 | 0.95 | 0.96 | 3 | 0.91 |
4rxn | 677 | 1.36 – 8.14 | 3 | -2.35 | -2.83 | 84.2 | 0.98 | 0.98 | 1 | 0.95 |
Average | 665 | 1.15 – 8.80 | -2.17 | -2.82 | 86.8 | 0.97 | 0.98 | 0.92 | ||
fisa | ||||||||||
1fc2 | 500 | 3.11 – 10.58 | 115 | -0.64 | -0.98 | 6 | 0.95 | 0.67 | 399 | 0.91 |
1hdd-C | 500 | 2.77 – 12.92 | 18 | -1.44 | -1.62 | 28 | 0.95 | 0.88 | 248 | 0.93 |
2cro | 500 | 4.29 – 12.60 | 109 | -0.66 | -1.7 | 26 | 0.74 | 0.75 | 98 | 0.62 |
4icb | 500 | 4.75 – 14.13 | 81 | -0.79 | -1.68 | 24 | 0.69 | 0.69 | 138 | 0.60 |
Average | 500 | 3.73 – 12.56 | -0.89 | -1.5 | 21 | 0.83 | 0.75 | 0.77 | ||
fisa_casp3 | ||||||||||
1bg8-A | 1,200 | 6.03 – 15.80 | 177 | -0.83 | -1.16 | 13.3 | 0.39 | 0.39 | 721 | 0.2 |
1bl0 | 971 | 3.63 – 18.17 | 44 | -1.34 | -2.03 | 57.7 | 0.74 | 0.73 | 129 | 0.7 |
1eh2 | 2,413 | 4.00 – 15.29 | 196 | -1.09 | -2.68 | 52.6 | 0.8 | 0.81 | 300 | 0.75 |
1jwe | 1,407 | 7.79 – 20.87 | 345 | -0.61 | -0.72 | 4.2 | -0.24 | -0.23 | 1298 | -0.23 |
l30 | 1,400 | 6.47 – 24.62 | 474 | -0.47 | -0.91 | 0 | 0.28 | 0.25 | N/A | 0.21 |
smd3 | 1,200 | 8.54 – 17.00 | 74 | -1.21 | -1.21 | 17.5 | 0.65 | 0.6 | 993 | 0.45 |
Average | 1,432 | 6.08 – 18.63 | -0.93 | -1.45 | 24.2 | 0.43 | 0.42 | 0.35 | ||
lattice_ssfit | ||||||||||
1beo | 2,000 | 7.00 – 15.61 | 6 | -2.52 | -2.52 | 30.5 | 0.46 | 0.45 | 1069 | 0.07 |
1ctf | 2,000 | 5.45 – 12.81 | 174 | -1.06 | -1.74 | 40 | 0.71 | 0.72 | 882 | 0.55 |
1dkt-A | 2,000 | 6.69 – 14.05 | 74 | -1.43 | -2 | 34 | 0.42 | 0.4 | 1987 | 0.18 |
1fca | 2,000 | 5.14 – 11.39 | 224 | -0.95 | -1.81 | 43 | 0.55 | 0.54 | 1287 | 0.35 |
1nkl | 2,000 | 5.27 – 13.64 | 264 | -0.88 | -2.19 | 20 | 0.54 | 0.56 | 1103 | 0.33 |
1pgb | 2,000 | 5.81 – 12.91 | 796 | -0.4 | -1.04 | 10 | 0.39 | 0.35 | 1840 | 0.27 |
1trl-A | 2,000 | 5.38 – 12.52 | 480 | -0.62 | -1.63 | 14.5 | 0.41 | 0.39 | 1458 | 0.3 |
4icb | 2,000 | 4.74 – 12.92 | 16 | -2.1 | -2.3 | 41 | 0.69 | 0.69 | 318 | 0.61 |
Average | 2,000 | 5.68 – 13.23 | -1.24 | -1.9 | 29.1 | 0.52 | 0.51 | 0.33 | ||
lmds | ||||||||||
1b0n-B | 497 | 2.45 – 6.03 | 70 | -0.85 | -0.85 | 2 | 0.14 | 0.16 | 468 | 0.15 |
1bba | 500 | 2.78 – 8.91 | 162 | -0.49 | -0.72 | 0 | 0.39 | 0.24 | 300 | 0.5 |
1ctf | 497 | 3.59 – 12.53 | 185 | -0.43 | -0.58 | 0 | 0.41 | 0.49 | 367 | 0.1 |
1dtk | 215 | 4.32 – 12.58 | 90 | -0.38 | -0.93 | 14 | 0.63 | 0.55 | 121 | 0.53 |
1fc2 | 500 | 3.99 – 8.45 | 245 | -0.31 | -0.7 | 4 | 0.46 | 0.22 | 488 | 0.25 |
1igd | 500 | 3.11 – 12.55 | 135 | -0.57 | -1.7 | 38 | 0.81 | 0.79 | 113 | 0.84 |
1shf-A | 437 | 4.39 – 12.35 | 19 | -1.36 | -1.36 | 13.7 | 0.15 | 0.16 | 211 | 0.18 |
2cro | 500 | 3.87 – 13.48 | 208 | -0.38 | -0.8 | 0 | 0.36 | 0.36 | 362 | 0.16 |
2ovo | 347 | 4.38 – 13.38 | 15 | -1.36 | -1.5 | 23.1 | 0.56 | 0.59 | 162 | 0.45 |
4pti | 343 | 4.94 – 13.18 | 119 | -0.46 | -1.28 | 14.6 | 0.67 | 0.52 | 250 | 0.63 |
unk | 500 | 6.68 – 13.94 | 190 | -0.42 | -0.46 | 0 | 0.25 | 0.07 | N/A | 0.07 |
Average | 440 | 4.05 – 11.58 | -0.64 | -0.99 | 9.9 | 0.44 | 0.38 | 0.35 | ||
semfold | ||||||||||
1ctf | 11,400 | 4.44 – 12.98 | 1,936 | -0.77 | -0.87 | 9.7 | 0.13 | 0.17 | 10252 | 0.05 |
1e68 | 11,360 | 2.98 – 12.53 | 6,388 | -0.25 | -0.27 | 14.5 | 0.19 | 0.13 | 2951 | 0.31 |
1eh2 | 11,440 | 5.32 – 15.07 | 1,068 | -1.03 | -1.41 | 21.9 | 0.24 | 0.21 | 3998 | 0.22 |
1khm | 21,080 | 3.84 – 14.77 | 8,992 | -0.37 | -0.67 | 5.9 | 0.1 | 0.1 | 13444 | 0.07 |
1nkl | 11,660 | 3.84 – 14.22 | 2,862 | -0.61 | -0.73 | 14.4 | 0.32 | 0.32 | 3992 | 0.32 |
1pgb | 11,280 | 4.67 – 13.01 | 3,650 | -0.49 | -0.59 | 7.4 | 0.09 | 0.11 | 11274 | 0.06 |
Average | 13,037 | 4.18 – 13.76 | -0.59 | -0.76 | 12.3 | 0.18 | 0.17 | 0.17 | ||
Rosetta | ||||||||||
1a32 | 1,610 | 0.92 – 16.89 | 352 | -0.66 | -1.02 | 19.3 | 0.89 | 0.93 | 290 | 0.87 |
1aa3 | 1,865 | 3.02 – 12.77 | 390 | -0.68 | -0.77 | 3.8 | 0.57 | 0.6 | 1 | 0.66 |
1afi | 1,824 | 2.24 – 15.14 | 26 | -1.85 | -2.22 | 42.8 | 0.92 | 0.94 | 201 | 0.95 |
1ail | 1,807 | 1.97 – 14.69 | 95 | -1.28 | -1.77 | 59.8 | 0.92 | 0.93 | 49 | 0.91 |
1am3 | 1,898 | 1.36 – 11.63 | 245 | -0.89 | -1.92 | 39 | 0.69 | 0.75 | 1 | 0.81 |
1bq9 | 1,825 | 2.59 – 15.73 | 303 | -0.78 | -1.88 | 30.1 | 0.41 | 0.47 | 1 | 0.68 |
1bw6 | 1,900 | 1.89 – 12.30 | 11 | -2.22 | -2.5 | 27.9 | 0.75 | 0.74 | 1 | 0.84 |
1cc5 | 1,892 | 6.41 – 26.78 | 280 | -0.83 | -1.06 | 30.7 | 0.46 | 0.46 | 1891 | 0.36 |
1cei | 1,897 | 4.57 – 16.34 | 185 | -1.01 | -2.8 | 51.1 | 0.82 | 0.84 | 255 | 0.75 |
1csp | 1,809 | 3.89 – 17.92 | 361 | -0.7 | -1.03 | 7.7 | 0.49 | 0.47 | 1 | 0.58 |
1ctf | 1,922 | 5.07 – 15.81 | 305 | -0.8 | -2.44 | 31.2 | 0.75 | 0.7 | 1 | 0.67 |
1dol | 1,871 | 3.77 – 14.87 | 100 | -1.27 | -1.27 | 17.1 | 0.37 | 0.4 | 1 | 0.6 |
1gab | 1,898 | 2.75 – 11.81 | 345 | -0.74 | -0.74 | 0.5 | 0.29 | 0.29 | 1 | 0.38 |
1hyp | 1,893 | 4.64 – 15.63 | 337 | -0.75 | -1.62 | 20.6 | 0.19 | 0.26 | 55 | 0.42 |
1kjs | 1,893 | 3.37 – 13.68 | 77 | -1.39 | -1.68 | 30.1 | 0.79 | 0.76 | 1 | 0.78 |
1lfb | 1,893 | 2.47 – 14.93 | 198 | -0.98 | -1.65 | 27.5 | 0.73 | 0.74 | 1 | 0.81 |
1msi | 1,894 | 5.84 – 14.52 | 107 | -1.25 | -1.58 | 32.7 | 0.47 | 0.49 | 1 | 0.59 |
1mzm | 1,934 | 3.68 – 15.08 | 443 | -0.64 | -0.66 | 1 | 0.05 | 0.1 | 191 | 0.19 |
1nkl | 1,898 | 2.73 – 12.74 | 208 | -0.96 | -1.41 | 24.2 | 0.58 | 0.54 | 1 | 0.58 |
1nre | 1,893 | 1.80 – 17.11 | 300 | -0.8 | -1.5 | 37 | 0.7 | 0.75 | 1 | 0.82 |
1orc | 1,883 | 2.88 – 15.08 | 343 | -0.74 | -1.09 | 20.2 | 0.57 | 0.57 | 2 | 0.65 |
1pgx | 1,851 | 5.03 – 16.75 | 465 | -0.6 | -0.6 | 0 | -0.19 | -0.17 | 1261 | -0.2 |
1pou | 1,898 | 2.28 – 17.68 | 322 | -0.77 | -2.13 | 46.9 | 0.59 | 0.64 | 1 | 0.77 |
1ptq | 1,885 | 5.42 – 12.23 | 368 | -0.71 | -1.29 | 11.7 | 0.12 | 0.09 | 1 | 0.41 |
1r69 | 1,733 | 2.26 – 12.58 | 218 | -0.9 | -1.03 | 30 | 0.73 | 0.76 | 1 | 0.74 |
1res | 1,723 | 1.89 – 9.15 | 475 | -0.56 | -0.57 | 0 | -0.13 | 0 | 334 | -0.17 |
1sro | 1,881 | 3.39 – 15.36 | 462 | -0.61 | -0.83 | 4.8 | 0.77 | 0.75 | 1 | 0.68 |
1tif | 1,849 | 2.61 – 11.56 | 464 | -0.6 | -1.46 | 15.1 | 0.59 | 0.53 | 1 | 0.61 |
1tuc | 1,894 | 4.49 – 16.85 | 37 | -1.71 | -2.16 | 35.9 | 0.66 | 0.66 | 1 | 0.69 |
1uba | 1,899 | 4.07 – 11.62 | 346 | -0.74 | -1.22 | 31.6 | 0.39 | 0.41 | 1 | 0.51 |
1utg | 1,897 | 3.36 – 16.50 | 535 | -0.55 | -0.73 | 18.5 | 0.51 | 0.5 | 1 | 0.65 |
1uxd | 1,896 | 1.12 – 10.13 | 181 | -1.02 | -1.21 | 25.8 | 0.61 | 0.58 | 1 | 0.68 |
1vcc | 1,857 | 3.85 – 16.90 | 64 | -1.46 | -3.27 | 41.5 | 0.76 | 0.78 | 1 | 0.6 |
1vif | 1,896 | 4.78 – 15.18 | 233 | -0.91 | -1.03 | 6.9 | 0.76 | 0.76 | 1 | 0.76 |
2ezh | 1,893 | 2.34 – 18.26 | 510 | -0.57 | -2.24 | 28.5 | 0.56 | 0.57 | 1 | 0.68 |
2fow | 1,834 | 4.03 – 13.89 | 59 | -1.49 | -2.22 | 39.3 | 0.46 | 0.54 | 1 | 0.64 |
2fxb | 1,800 | 7.46 – 19.02 | 58 | -1.49 | -2.3 | 47.8 | 0.75 | 0.75 | 1 | 0.48 |
2pdd | 1,740 | 2.33 – 10.02 | 934 | -0.27 | -1.09 | 17.8 | 0.21 | 0.23 | 1 | 0.53 |
2ptl | 1,835 | 2.21 – 15.45 | 16 | -2.06 | -2.22 | 38.2 | 0.86 | 0.86 | 1 | 0.78 |
5icb | 1,870 | 2.98 – 13.68 | 527 | -0.55 | -2.49 | 30 | 0.59 | 0.62 | 1 | 0.7 |
5pti | 1,853 | 4.88 – 15.31 | 586 | -0.5 | -1.28 | 8.6 | 0.24 | 0.2 | 1 | 0.6 |
Average | 1,858 | 3.38 – 14.87 | -0.96 | -1.56 | 25.2 | 0.54 | 0.56 | 0.61 |