Table 1.

Pharmacophore model performance metrics.

Metrics calculated based on the training set
Overlap	Score reflecting volume and functional group overlap of actives, maximum equal to number of actives
Accuracy	Fraction of compounds correctly matched (actives) and not matched (inactives)
Metrics calculated based on the test set
Matches	Compounds selected by the pharmacophore model
True positives	Matches confirmed by experimental assay to be active
True negatives	Non-matches confirmed by experimental assay to be inactive
False positives	Matches confirmed by experimental assay to be inactive
False negatives	Non-matches confirmed by experimental assay to be active
Hit rate	Percent of matches that are true positives
Recovery percent	Percent of total actives (true positives + false negatives) in the matches list
Miss percent	Percent of total actives not in the matches list
Negative accuracy	Fraction of inactives not matching the pharmacophore model