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Table 3 PRANK vs. simpler rescoring methods

From: Improving protein-ligand binding site prediction accuracy by classification of inner pocket points using local features

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
  1. PLB - rescoring by the Propensity for Ligand Binding index based on amino acid composition of pockets [29].
  2. VOL - rescoring by approximate volume.
  3. **cross-validation results.
  4. 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.
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