Table 3.
Comparison of performance of the RAPDF and self-RAPDF on 83 decoy sets grouped by their generation methods.
| Protein (PDB code) | RAPDF | Self-RAPDF | ||||||
| log PB1 | log PB10 | F.E.(%) | C.C. | log PB1 | log PB10 | F.E.(%) | C.C. | |
| 4state_reduced | ||||||||
| 1ctf | -2.50 | -2.80 | 57.14 | 0.73 | -2.32 | -2.80 | 79.37 | 0.89 |
| 1r69 | -1.93 | -2.83 | 42.96 | 0.70 | -2.83 | -2.83 | 72.59 | 0.88 |
| 1sn3 | -1.44 | -1.97 | 40.91 | 0.47 | -2.82 | -2.82 | 84.85 | 0.89 |
| 2cro | -2.05 | -2.23 | 45.99 | 0.76 | -2.83 | -2.83 | 78.64 | 0.92 |
| 3icb | -1.40 | -2.34 | 68.91 | 0.85 | -2.21 | -2.51 | 81.16 | 0.92 |
| 4pti | -0.64 | -2.54 | 23.29 | 0.49 | -1.80 | -2.84 | 87.34 | 0.89 |
| 4rxn | -0.43 | -2.35 | 53.18 | 0.57 | -2.53 | -2.83 | 78.29 | 0.88 |
| fisa | ||||||||
| 1fc2 | -0.86 | -0.86 | 4.00 | 0.52 | -0.39 | -0.98 | 6.00 | 0.77 |
| 1hdd-C | -2.40 | -2.40 | 44.00 | 0.55 | -0.52 | -1.80 | 30.00 | 0.74 |
| 2cro | -2.40 | -2.40 | 26.00 | 0.19 | -0.66 | -1.70 | 24.00 | 0.29 |
| 4icb | -0.71 | -1.30 | 20.00 | 0.20 | -0.67 | -1.12 | 26.00 | 0.46 |
| fisa_casp3 | ||||||||
| 1bg8-A | -0.94 | -1.90 | 15.00 | 0.16 | -0.80 | -1.25 | 9.17 | 0.09 |
| 1bl0 | -0.28 | -2.69 | 12.36 | 0.18 | -0.17 | -0.20 | 47.37 | 0.59 |
| 1eh2 | -1.11 | -1.80 | 18.65 | 0.25 | -0.65 | -2.91 | 43.93 | 0.53 |
| 1jwe | -0.42 | -1.19 | 2.84 | -0.14 | -0.12 | -0.38 | 1.42 | -0.23 |
| l30 | -0.27 | -1.65 | 12.14 | -0.12 | -0.58 | -0.86 | 0.00 | 0.18 |
| smd3 | 0.00 | -0.57 | 4.17 | -0.20 | -0.59 | -1.48 | 15.83 | 0.28 |
| lattice_ssfit | ||||||||
| 1beo | -0.86 | -1.49 | 7.00 | -0.02 | -2.52 | -2.52 | 12.00 | 0.09 |
| 1ctf | -0.15 | -1.55 | 10.00 | -0.06 | -1.40 | -1.48 | 23.50 | 0.15 |
| 1dkt-A | -0.31 | -3.00 | 10.50 | -0.04 | -1.43 | -2.00 | 25.00 | 0.15 |
| 1fca | -0.07 | -1.19 | 8.00 | 0.00 | -1.32 | -1.33 | 23.00 | 0.13 |
| 1nkl | -0.05 | -0.96 | 5.00 | -0.19 | -0.88 | -1.54 | 7.50 | -0.01 |
| 1pgb | -0.16 | -0.67 | 10.00 | -0.07 | -0.40 | -0.40 | 8.50 | 0.04 |
| 1trl-A | -0.45 | -1.10 | 7.50 | -0.07 | -0.62 | -1.63 | 12.00 | 0.09 |
| 4icb | -1.82 | -1.82 | 21.50 | -0.01 | -1.76 | -2.70 | 27.00 | 0.20 |
| lmds | ||||||||
| 1b0n-B | -0.06 | -1.44 | 6.04 | -0.21 | -0.85 | -2.00 | 16.10 | 0.10 |
| 1bba | -0.38 | -1.85 | 16.00 | 0.23 | -0.41 | -0.49 | 0.00 | 0.15 |
| 1ctf | -0.32 | -2.40 | 10.06 | 0.26 | -0.38 | -0.60 | 0.00 | 0.39 |
| 1dtk | -0.14 | -0.97 | 4.65 | 0.04 | -0.38 | -1.05 | 9.30 | 0.41 |
| 1fc2 | -0.62 | -2.10 | 8.00 | 0.02 | -0.20 | -0.62 | 6.00 | 0.27 |
| 1igd | -1.18 | -2.70 | 22.00 | 0.08 | -0.57 | -1.52 | 28.00 | 0.68 |
| 1shf-A | -0.10 | -0.85 | 11.44 | -0.03 | -1.36 | -1.36 | 13.73 | 0.14 |
| 2cro | -0.10 | -0.36 | 6.00 | -0.22 | -0.27 | -0.39 | 0.00 | -0.19 |
| 2ovo | -0.58 | -0.68 | 14.41 | 0.18 | -1.50 | -1.50 | 23.05 | 0.51 |
| 4pti | -0.05 | -1.93 | 23.32 | 0.09 | -0.46 | -1.28 | 29.15 | 0.53 |
| unk | -0.70 | -1.27 | 16.00 | 0.17 | -0.46 | -0.85 | 6.00 | 0.10 |
| semfold | ||||||||
| 1ctf | -0.39 | -0.48 | 11.05 | 0.07 | -0.34 | -0.40 | 8.86 | 0.10 |
| 1e68 | -2.62 | -2.68 | 25.17 | 0.13 | -0.17 | -2.68 | 27.29 | 0.13 |
| 1eh2 | -0.08 | -0.29 | 14.51 | 0.07 | -0.47 | -0.55 | 19.84 | 0.10 |
| 1khm | -0.09 | -0.36 | 12.48 | 0.01 | -0.34 | -0.38 | 9.01 | -0.03 |
| 1nkl | -3.11 | -3.11 | 17.67 | 0.10 | -2.55 | -2.77 | 20.07 | 0.21 |
| 1pgb | -0.05 | -0.59 | 15.07 | 0.05 | -0.53 | -0.76 | 15.51 | 0.10 |
| Rosetta | ||||||||
| 1a32 | -0.09 | -0.31 | 0.00 | -0.22 | -0.97 | -1.41 | 44.10 | 0.89 |
| 1aa3 | -0.14 | -0.69 | 9.65 | -0.06 | -0.52 | -0.70 | 6.97 | 0.44 |
| 1afi | -0.54 | -2.22 | 27.96 | 0.45 | -2.18 | -2.78 | 52.08 | 0.91 |
| 1ail | -0.07 | -0.33 | 5.53 | 0.01 | -1.77 | -3.26 | 57.55 | 0.71 |
| 1am3 | -0.08 | -0.27 | 9.48 | 0.06 | -2.38 | -2.38 | 44.26 | 0.85 |
| 1bq9 | -0.38 | -1.11 | 14.80 | 0.04 | -1.88 | -1.90 | 25.75 | 0.23 |
| 1bw6 | -0.14 | -0.89 | 18.42 | 0.49 | -1.04 | -2.22 | 44.21 | 0.75 |
| 1cc5 | -0.42 | -2.37 | 8.99 | 0.02 | -0.20 | -2.37 | 24.31 | 0.24 |
| 1cei | -0.27 | -0.30 | 13.71 | 0.02 | -1.18 | -2.38 | 45.86 | 0.49 |
| 1csp | -0.53 | -1.30 | 11.06 | 0.04 | -0.58 | -1.47 | 16.58 | 0.31 |
| 1ctf | -0.04 | -0.56 | 8.85 | -0.06 | -0.27 | -1.64 | 21.33 | 0.31 |
| 1dol | -0.57 | -1.58 | 20.31 | 0.08 | -0.69 | -1.58 | 24.59 | 0.27 |
| 1gab | -0.11 | -1.49 | 14.75 | -0.04 | -0.64 | -0.70 | 0.53 | 0.16 |
| 1hyp | -0.34 | -0.34 | 3.17 | -0.29 | -0.89 | -1.09 | 8.98 | -0.24 |
| 1kjs | -0.91 | -1.56 | 20.07 | 0.44 | -1.39 | -2.16 | 36.45 | 0.74 |
| 1lfb | -0.17 | -0.55 | 5.28 | -0.02 | -1.86 | -2.02 | 43.85 | 0.64 |
| 1msi | -1.35 | -1.35 | 16.90 | 0.11 | -0.83 | -1.50 | 25.87 | 0.19 |
| 1mzm | -0.81 | -0.81 | 4.65 | -0.19 | -0.32 | -0.85 | 0.52 | -0.13 |
| 1nkl | -1.07 | -1.35 | 20.55 | 0.10 | -0.96 | -1.03 | 17.39 | 0.53 |
| 1nre | -0.30 | -0.37 | 3.17 | 0.05 | -0.94 | -2.68 | 50.71 | 0.74 |
| 1orc | -0.03 | -0.43 | 0.00 | -0.35 | -0.74 | -1.03 | 21.24 | 0.43 |
| 1pgx | -0.07 | -0.38 | 1.08 | -0.55 | -0.37 | -0.47 | 1.08 | -0.39 |
| 1pou | -0.29 | -1.65 | 11.06 | 0.05 | -2.13 | -2.80 | 54.27 | 0.49 |
| 1ptq | -0.12 | -1.39 | 16.98 | 0.07 | -0.87 | -1.31 | 9.55 | 0.01 |
| 1r69 | -0.51 | -1.20 | 19.04 | 0.14 | -1.82 | -1.82 | 53.09 | 0.61 |
| 1res | -0.95 | -1.50 | 13.35 | 0.00 | -0.41 | -0.57 | 0.00 | 0.01 |
| 1sro | -0.55 | -1.11 | 15.95 | 0.15 | -0.66 | -0.84 | 18.08 | 0.68 |
| 1tif | -0.53 | -1.93 | 15.68 | 0.11 | -1.17 | -1.93 | 42.19 | 0.61 |
| 1tuc | -0.55 | -0.78 | 11.09 | 0.18 | -1.11 | -1.90 | 33.79 | 0.71 |
| 1uba | -0.56 | -0.74 | 4.74 | -0.10 | -0.63 | -2.05 | 22.12 | 0.19 |
| 1utg | -0.16 | -1.42 | 7.38 | 0.02 | -0.73 | -0.80 | 26.36 | 0.56 |
| 1uxd | -0.29 | -0.58 | 13.19 | 0.07 | -1.20 | -2.43 | 29.54 | 0.79 |
| 1vcc | -0.05 | -0.80 | 13.46 | 0.17 | -1.46 | -2.42 | 29.08 | 0.47 |
| 1vif | -0.24 | -3.28 | 37.45 | 0.39 | -0.97 | -0.97 | 11.08 | 0.74 |
| 2ezh | -0.53 | -1.13 | 26.41 | 0.40 | -0.86 | -1.06 | 36.98 | 0.78 |
| 2fow | -0.52 | -0.57 | 9.27 | 0.13 | -1.25 | -1.39 | 25.63 | 0.51 |
| 2fxb | -0.43 | -2.65 | 11.67 | 0.05 | -0.87 | -2.65 | 29.44 | 0.40 |
| 2pdd | -0.01 | -2.01 | 16.09 | -0.04 | -1.01 | -1.56 | 38.51 | 0.45 |
| 2ptl | -0.35 | -2.06 | 20.71 | 0.17 | -1.65 | -2.06 | 39.78 | 0.72 |
| 5icb | -0.57 | -0.99 | 21.93 | 0.40 | -1.02 | -2.57 | 32.62 | 0.66 |
| 5pti | -0.12 | -0.34 | 1.08 | -0.15 | -0.50 | -1.28 | 9.17 | 0.09 |
For legends please refer to Table 2. The self-RAPDF has better performance than RAPDF in terms of log PB1 (62/83 decoy sets), log PB10 (56/83 decoy sets), F.E. (63/83 decoy sets) and C.C. (76/83 decoy sets).