Table 8.
Benchmarking based on three standard decoy sets from the Decoys 'R' Us database
| 4state_reduced | Lattice_ssfit | LMDS | ||||
| Method | Z-score | Rank 1 | Z-score | Rank 1 | Z-score | Rank 1 |
| ModFOLD | 3.74 | 5/7 | 10.12 | 7/8 | 3.33 | 5/10 |
| PROQ-LG | 3.73 | 3/7 | 11.19 | 7/8 | 1.91 | 1/10 |
| PROQ-MX | 3.44 | 4/7 | 18.15 | 7/8 | 2.15 | 3/10 |
| MODCHECK | 2.20 | 3/7 | 5.05 | 8/8 | 1.64 | 3/10 |
| ModSSEA | 1.95 | 3/7 | 4.31 | 6/8 | 1.62 | 3/10 |
Rank 1 – the number of native structures correctly ranked first by each method out of the total proteins in decoy set; Z-score – the average Z-scores calculated as the distance in standard deviations from the MQAP score of the native structure to the mean score of the decoy set.