Negative dataset (Quorum sensing peptides taken from QSPpred and cross referenced with Quorumpeps database)

The 18 inactive peptides obtained from the BaAMPs database could not constitute a substantive negative dataset and therefore quorum-sensing peptides (QSPs) were selected for this purpose. QSPs are oligopeptides used as autoinducing molecules by Gram positive bacteria in intra-species QS known to enable the biofilm phenotype. A total of 220 unique QSPs were retrieved from QSPpred web server comprising of positive (training + independent) datasets, from which one pyrrolysine (O) containing peptide sequence was removed. The remaining 219 peptides were then manually screened and simultaneously cross-referenced with the Quorumpeps database for corresponding entries. Entries were missing for 30 peptides in Quorumpeps, 68 peptides had cyclic structures and 7 amidated linear peptides were RNAIII inhibiting (RIPs) (Fig. 1B). Out of the remaining 114 non-amidated linear peptides, 26 were identified to have antimicrobial or biofilm-inhibitory activity (EDFs, RIPs, RBPs, bacteriocin inducing) and were excluded to yield the final 88 peptide sequences which were used to train the models. Additionally, 10 QSPs were retrieved from QSPpred (with missing Quorumpeps entries) and curated from published literature as the negative independent dataset.