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Table 3 Comparison of predictive performance on COACH420 and HOLO4K datasets

From: P2Rank: machine learning based tool for rapid and accurate prediction of ligand binding sites from protein structure

  COACH420 HOLO4K
Top-n Top-(n+2) Top-n Top-(n+2)
Fpocket 56.4 68.9 52.4 63.1
Fpocket+PRANKa 63.6 76.5 62.0 71.0
SiteHound 53.0 69.3 50.1 62.1
MetaPocket 2.0 63.4 74.6 57.9 68.6
DeepSite 56.4 63.4 45.6 48.2
P2Rank[protrusion]b 64.2 73.0 59.3 67.7
P2Rank 72.0 78.3 68.6 74.0
  1. The numbers represent identification success rate [%] measured by DCCcriterion (distance from pocket center to closest ligand atom) with 4 Å threshold considering only pockets ranked at the top of the list (n is the number of ligands in considered structure)
  2. These methods failed to produce predictions for some portion of input proteins. Here we display success rates calculated only based on subsets of proteins, on which they finished successfully. Detailed, pairwise comparison with P2Rank on the exact subsets can be found in the Additional file 1.
  3. aPredictions of Fpocket re-scored by PRANK algorithm (which is included in P2Rank software package)
  4. bReduced version of P2Rank that uses only single geometric feature: protrusion