Table 3. A selected list of 16 binary protein complexes from the “difficult” and “medium difficult” category of the protein docking benchmark dataset version 4.0 [39].
| PDB-ID ChainId1:ChainId2 | Difficulty class(M = Medium Difficulty,D = Difficult) | L-RMSD of best modelwithout XLs | Total number of virtualinter-protein XLs | Lowest L-RMSD amongthe 10 best modelsusing 7 randominter-protein XLs | L-RMSD of best modelusing 7 random inter-protein XLs |
| 1MQ8 A:B | M | 55.1 | 23 | 4.3 | 4.3 |
| 1JK9 A:B | D | 40.3 | 31 | 6.8 | 7.2 |
| 2CFH A:C | M | 38.2 | 16 | 7.1 | 7.6 |
| 2NZ8 A:B | M | 24.1 | 35 | 7.9 | 7.9 |
| 1ATN A:D | D | 44.7 | 9 | 8.0 | 8.0 |
| 1FQ1 A:B | D | 31.5 | 28 | 8.0 | 8.0 |
| 1I2M A:B | M | 30.9 | 25 | 8.4 | 8.4 |
| 2Z0E A:B | M | 25.0 | 12 | 7.5 | 8.5 |
| 1F6M A:C | D | 52.1 | 20 | 6.0 | 8.6 |
| 1BKD R:S | D | 34.5 | 43 | 9.0 | 9.0 |
| 2J7P A:D | M | 39.8 | 31 | 9.8 | 9.8 |
| 1HE8 B:A | M | 90.8 | 38 | 10.7 | 10.7 |
| 1IBR A:B | D | 47.3 | 49 | 13.0 | 13.0 |
| 1Y64 A:B | D | 55.8 | 65 | 19.7 | 24.9 |
| 1IRA Y:X | D | 35.7 | 26 | 34.4 | 34.4 |
| 1H1V A:G | D | 83.0 | 20 | 42.4 | 42.4 |
Each complex has more than 7 predicted (virtual) inter-protein cross-links and was employed to test the impact of cross-links on protein docking calculations. Best models correspond to the models with the shortest mean SAS distance for all 7 cross-links. L-RMSD corresponds to the RMSD value among the smaller protein partners also known as ligands.