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Table 1 The comparison of the performance of the Morgan2 (ECFP4) and b-QAFFP fingerprints for similarity searching for 69 HET data sets

From: QSAR-derived affinity fingerprints (part 1): fingerprint construction and modeling performance for similarity searching, bioactivity classification and scaffold hopping

FP

Morgan2

b-QAFFP

AD

No

Yes

Cutoff

5

6

7

8

5

6

7

8

AUC

0.66 ± 0.01

0.63 ± 0.01

0.63 ± 0.01

0.65 ± 0.01

0.58 ± 0.01

0.70 ± 0.01

0.62 ± 0.01

0.63 ± 0.01

0.56 ± 0.01

EF5

6.41 ± 0.40

3.67 ± 0.25

4.52 ± 0.33

4.50 ± 0.30

2.27 ± 0.16

5.82 ± 0.34

4.65 ± 0.32

3.97 ± 0.26

1.76 ± 0.12

  1. 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 HET data sets with their standard errors of the mean. The b-QAFFP fingerprint is 384 bits long