Deep learning improves antimicrobial peptide recognition

MOTIVATION: Bacterial resistance to antibiotics is a growing concern. Antimicrobial peptides (AMPs), natural components of innate immunity, are popular targets for developing new drugs. Machine learning methods are now commonly adopted by wet-laboratory researchers to screen for promising candidates. RESULTS: In this work, we utilize deep learning to recognize antimicrobial activity. We propose a neural network model with convolutional and recurrent layers that leverage primary sequence composition. Results show that the proposed model outperforms state-of-the-art classification models on a comprehensive dataset. By utilizing the embedding weights, we also present a reduced-alphabet representation and show that reasonable AMP recognition can be maintained using nine amino acid types. AVAILABILITY AND IMPLEMENTATION: Models and datasets are made freely available through the Antimicrobial Peptide Scanner vr.2 web server at www.ampscanner.com. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.