Table 2.

The comparison of the performance of the Morgan2 (ECFP4) and b-QAFFP fingerprints for similarity searching for 37 HOM data sets

FP	Morgan2	b-QAFFP
AD	–	No				Yes
Cutoff	–	5	6	7	8	5	6	7	8
AUC	0.57 ± 0.02	0.61 ± 0.02	0.58 ± 0.03	0.61 ± 0.02	0.57 ± 0.02	0.65 ± 0.02	0.59 ± 0.02	0.61 ± 0.02	0.56 ± 0.02
EF5	4.09 ± 0.42	3.44 ± 0.30	3.52 ± 0.47	3.88 ± 0.54	2.33 ± 0.24	4.67 ± 0.53	3.56 ± 0.51	3.39 ± 0.53	1.81 ± 0.21

Model AD was estimated by an ICP. Affinities predicted to lie outside model AD were encoded by zeros. Various affinity cutoffs were used to construct the b-QAFFP fingerprint. Best results are shown in a column in italic. Data shown are averages over all HOM data sets with their standard errors of the mean. The b-QAFFP fingerprint is 402 bits long