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

Table 2 Results of integrating PDBinder with Q-SiteFinder

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.

ISSN: 1471-2105