Deep learning regression model for antimicrobial peptide design

Abstract Antimicrobial peptides (AMPs) are naturally occurring or synthetic peptides that show promise for treating antibiotic-resistant pathogens. Machine learning techniques are increasingly used to identify naturally occurring AMPs, but there is a dearth of purely computational methods to design novel effective AMPs, which would speed AMP development. We collected a large database, Giant Repository of AMP Activities (GRAMPA), containing AMP sequences and associated MICs. We designed a convolutional neural network to perform combined classification and regression on peptide sequences to quantitatively predict AMP activity against Escherichia coli . Our predictions outperformed the state of the art at AMP classification and were also effective at regression, for which there were no publicly available comparisons. We then used our model to design novel AMPs and experimentally demonstrated activity of these AMPs against the pathogens E. coli, Pseudomonas aeruginosa , and Staphylococcus aureus . Data, code, and neural network architecture and parameters are available at https://github.com/zswitten/Antimicrobial-Peptides .