Table 2

Results of integrating PDBinder with Q-SiteFinder

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


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.

Bianchi et al. BMC Bioinformatics 2012 13(Suppl 4):S17   doi:10.1186/1471-2105-13-S4-S17

Open Data