Table 1.
The information of the datasets utilized in this study
| Dataset | Re-docked poses | Cross-docked poses | ||||||
|---|---|---|---|---|---|---|---|---|
| Complexes | Poses | Positives | Negatives | Complexes | Poses | Positives | Negatives | |
| PDBbind-ReDocked | 4057 | 83,876 | 39,978 | 43,898 | – | – | – | – |
| PDBbind-ReDocked-Refined | 3767 | 77,922 | 37,114 | 40,808 | – | – | – | – |
| PDBbind-ReDocked-Core | 290 | 5954 (5664)a | 2864 (2574) | 3090 | – | – | – | – |
| CASF-Docking | 285b | 22,777 (22,492) | 5494 (5209) | 17,283 | – | – | – | – |
| PDBbind-CrossDocked-Core-s | 285 | 5551 | 2565 | 2,986 | 1058 | 20,859 | 5872 | 14,987 |
| PDBbind-CrossDocked-Core-g | 282 | 4795 | 1596 | 3,199 | 1030 | 17,814 | 3768 | 14,046 |
| PDBbind-CrossDocked-Core-v | 285 | 5693 | 301 | 5,392 | 1058 | 21,145 | 740 | 20,405 |
| PDBbind-CrossDocked-Refined | 3767 | 77,839 (74,072) | 37,028 (33,261) | 40,811 | 90,002 | 1,874,433 | 1,499,702 | 374,731 |
| PDBbind-CrossDocked-Refined*c | 3767 | 77,839 (74,072) | 37,028 (33,261) | 40,811 | 90,002 | 1,731,351 | 1,428,161 | 303,190 |
aThe number in bracket refers to the number after removing the crystal poses
bThe core set of original PDBbind 2016 has 290 complexes belonging to 58 clusters, while only 285 are remained when constructing the CASF because there is a duplicated cluster
cThe set eliminates the cross-native poses