Table 1. Prediction performance of the InterEvDock2 server on 812 complexes of the PPI4DOCK benchmark, split into four levels of difficulty: very easy, easy, hard and very hard.
| All | Very easy | Easy | Hard | Very hard | ||
|---|---|---|---|---|---|---|
| Number of cases | 812 | 174 | 498 | 118 | 22 | |
| Top 10 success rate | InterEvScore | 171 (21%) | 44 (25%) | 115 (23%) | 11 (9%) | 1 (5%) |
| SOAP_PP | 194 (24%) | 55 (32%) | 126 (25%) | 12 (10%) | 1 (5%) | |
| FRODOCK 2.1 | 164 (20%) | 55 (32%) | 102 (20%) | 5 (4%) | 2 (9%) | |
| InterEvDock2 consensus | 239 (29%) | 75 (43%) | 150 (30%) | 13 (11%) | 1 (5%) | |
| Zdock 3.0.2 | 126 (15%) | 33 (19%) | 83 (17%) | 9 (8%) | 1 (5%) | |
| Residue interface prediction (≥1 correct in top 5 receptor OR top 5 ligand) | InterEvDock2 | 735 (91%) | 160 (92%) | 450 (90%) | 103 (87%) | 22 (100%) |
| Zdock3.0.2 | 680 (84%) | 145 (83%) | 427 (86%) | 91 (77%) | 17 (79%) | |
| Residue interface prediction (≥1 correct in top 5 receptor AND top 5 ligand) | InterEvDock2 | 414 (51%) | 103 (59%) | 263 (53%) | 39 (33%) | 9 (41%) |
| Zdock3.0.2 | 345 (43%) | 76 (44%) | 228 (46%) | 33 (28%) | 8 (34%) | |
| Residue interface prediction (≥1 correct in top 1 receptor OR top 1 ligand) | InterEvDock2 | 613 (75%) | 140 (80%) | 385 (77%) | 71 (60%) | 17 (77%) |
| Zdock3.0.2 | 532 (66%) | 111 (64%) | 344 (69%) | 64 (54%) | 13 (58%) | |
| Residue interface prediction (≥1 correct in top 1 receptor AND top 1 ligand) | InterEvDock2 | 278 (34%) | 75 (43%) | 184 (37%) | 17 (14%) | 2 (9%) |
| Zdock3.0.2 | 195 (24%) | 44 (25%) | 133 (27%) | 15 (12%) | 3 (14%) |
The benchmark is made of the 812 targets of the PPI4DOCK benchmark (1417 cases) (37) for which pairs of co-evolved MSAs with more than 10 sequences could be obtained and FRODOCK 2.1 (13) was able to generate at least one acceptable or better decoy (44) among the top 50 000 decoys. In the upper part of the table, top 10 success rates are reported as the number of cases (and percentage between brackets) for which at least one model out of 10 is an acceptable or better solution. Assessed methods are InterEvScore (32), SOAP-PP (34), FRODOCK 2.1 (13), InterEvDock2 consensus (this work and (17)) and Zdock3.0.2 (45). In the lower part of the table, the number (and percentage) of cases for which at least one residue out of the top 10 or top 2 residues was correctly predicted as present in the complex interface is assessed for InterEvDock2 and Zdock3.0.2 (details are provided in the Supplementary Data). The best results for each category are highlighted in bold.