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Table 2 Results of integrating PDBinder with Q-SiteFinder

From: Identification of binding pockets in protein structures using a knowledge-based potential derived from local structural similarities

  SENS SPEC PPV MCC  
PDBinder (1) 0.295 0.983 0.413 0.313 HOLO
Q-siteFinder (2) 0.466 0.934 0.279 0.306  
(1) AND (2) 0.154 0.997 0.483 0.245  
(1) OR (2) 0.622 0.913 0.286 0.365  
PDBinder 0.251 0.984 0.372 0.271 APO
Q-siteFinder (2) 0.324 0.931 0.200 0.199  
(1) AND (2) 0.098 0.997 0.375 0.168  
(1) OR (2) 0.497 0.909 0.231 0.280  
  1. Integration of PDBinder with Q-SiteFinder. These results refer to the Apo/Holo Test Set. The first two rows detail the performance values achieved by PDBinder (1) and Q-SiteFinder (2) alone. The third row reports the results obtained if a residue is considered positive when it is predicted by both methods. The fourth row details the opposite situation in which a residue is considered positive when it is predicted by either method. The last row reports the results obtained with the two threshold systems. We performed a ten-fold cross validation to derive two different propensity thresholds, one for the residues predicted as positive by Q-SiteFinder and the other one for the negatives. The results are the average of the ten cross validation runs ± the standard error.