Evaluation of different binding site comparison tools with respect to the data set of successful applications.

A-C) The ROC curves for residue- (A), surface- (B), and interaction-based (C) comparison methods. The name of the tool is colored according to its corresponding ROC curve. The binding site comparison tools are sorted in descending order with respect to the AUC. (A) SiteAlign yielded a slightly better AUC if the distance d1 was used (thin line). (B) The best AUC values for ProBis, Shaper, Shaper(PDB), VolSite/Shaper, VolSite/Shaper(PDB), SiteEngine, and SiteHopper resulted from the scoring measures Zscore, Tanimoto (color), Tanimoto (color), Tanimoto (color), Tanimoto (color), TotalScore, and ShapeTanimoto, respectively (thin lines). D-F) EFs for residue- (D), surface- (E), and interaction-based (F) comparison methods. A linear color gradient ranging from white for the highest value to gray to black for the lowest value was applied for the EFs at different percentages of screened data set.