Table 5.
VLS performance and 3DAC prediction accuracy of ALiBERO-selected pocket conformer sets that better separate ligands from decoys.
| ALiBERO-selected pocket variants for ligands - decoys separation | ||||
|---|---|---|---|---|
|
| ||||
| Protein | CDK2 | THRB | HS90A | FA10 |
| #3DAC pairs | 26 | 24 | 11 | 11 |
| ligands | 36 | 28 | 17 | 12 |
| decoys | 2053 | 1490 | 970 | 594 |
|
| ||||
| Best pockets | 1h1s+1h01+2r3j | 3dhk+3egk+2anm | 3k97+2cct | 2p94+2vwm |
| combination | (+ 2xmy/2r3h/2vtm/1y8y) | (+ 1nt1+3f68) | 3k97+2vcj | (+2vwl) |
|
| ||||
| ROC | 0.85 (0.84) | 0.94 (0.95) | 0.72 (0.72) | 0.83 (0.83) |
| NSQ_AUC | 0.55 (0.55) | 0.73 (0.79) | 0.33 (0.34) | 0.51 (0.52) |
|
| ||||
| 3DAC separation from ALiBERO-selected pocket variants | ||||
|
| ||||
| no cut-off | 20/26 (77%) | 17/24 (71%) | 8/17 (47%) | 8/11 (73%) |
| CS = 0.74 | CS = 0.67 | CS = 0.43 | CS = 0.70 | |
|
| ||||
| 2.8 units cut-off | 18/26 (69%) | 15/24 (63%) | 4/17 (24%) | 6/11 (55%) |