Table 3.
PRANK vs. simpler rescoring methods
| Dataset | Top-n [%] | All [%] | PRANK [%] | Δ PRANK | PLB [%] | Δ PLB | VOL [%] | Δ VOL |
|---|---|---|---|---|---|---|---|---|
| Fpocket predictions | ||||||||
| CHEN11 | 47.9 | 71 | 58.8** | +10.6 | 49.8 | +1.9 | 34.5 | -13.4 |
| ASTEX | 58 | 81.1 | 63.6 | +5.6 | 56.6 | -1.4 | 32.2 | -25.9 |
| DT198 | 37.5 | 80.2 | 56.2 | +18.8 | 43.2 | +5.7 | 19.3 | -18.2 |
| MP210 | 56.6 | 78.8 | 67.7 | +11.1 | 54.5 | -2.1 | 30.6 | -26 |
| B48 | 74.1 | 92.6 | 81.5 | +7.4 | 72.2 | -1.9 | 42.6 | -31.5 |
| U48 | 53.7 | 88.9 | 77.8 | +24.1 | 66.7 | +13 | 31.5 | -22.2 |
| ConCavity predictions | ||||||||
| CHEN11 | 47.9 | 52.3 | 50.7** | +2.8 | 50.4 | +2.5 | 50.2 | +2.3 |
| ASTEX | 55.2 | 65.7 | 62.9 | +7.7 | 62.9 | +7.7 | 63.6 | +8.4 |
| DT198 | 45.8 | 65.6 | 61.5 | +15.6 | 56.8 | +10.9 | 59.4 | +13.5 |
| MP210 | 57.4 | 68.2 | 66.1 | +8.7 | 64.9 | +7.3 | 64.6 | +6.9 |
| B48 | 66.7 | 81.5 | 77.8 | +11.1 | 79.6 | +13 | 75.9 | +9.3 |
| U48 | 64.8 | 77.8 | 74.1 | +9.3 | 75.9 | +11.1 | 70.4 | +5.6 |
PLB - rescoring by the Propensity for Ligand Binding index based on amino acid composition of pockets [29].
VOL - rescoring by approximate volume.
**cross-validation results.
The number presented for rescoring methods (columns: PRANK,PLB,VOL) is the success rate considering Top-n predicted pockets measured by DCA criterion with 4 Å threshold.