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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