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Table 4 The average number of ACSKs per an assay (and its standard error of the mean SEM) in 22 CLASS sets revealed by the Morgan2, rv-QAFFP and b-QAFFP fingerprints

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

FP Morgan2 rv-QAFFP b-QAFFP
AD   No Yes No Yes
Cutoff 5 6 7 8 5 6 7 8
Average 39.27 41.41 41.45 48.40 47.80 48.89 66.14 48.41 47.89 48.54 67.58
SEM 8.25 8.51 8.68 10.26 10.47 11.18 16.02 10.37 10.54 10.88 16.84
  1. Model AD was estimated by an ICP with the confidence level of 90%. rv-QAFFP models were trained using raw data. Considering AD for rv-QAFFP means that if the prediction interval width was larger than ± 2.0, the prediction was regarded unreliable and was replaced by the average of all reliably predicted affinities. Various affinity cutoffs were used to construct the b-QAFFP fingerprint. Affinities predicted to lie outside model AD were encoded by zeros. Data shown are averages over 22 CLASS data sets with their standard errors of the mean (SEM). Both rv-QAFFP and b-QAFFP fingerprints are 440 bits long. The recommended settings are shown in columns in italic