CNN-PepPred: an open-source tool to create convolutional NN models for the discovery of patterns in peptide sets—application to peptide–MHC class II binding prediction

SUMMARY: The ability to unveil binding patterns in peptide sets has important applications in several biomedical areas, including the development of vaccines. We present an open-source tool, CNN-PepPred, that uses convolutional neural networks to discover such patterns, along with its application to peptide–HLA class II binding prediction. The tool can be used locally on different operating systems, with CPUs or GPUs, to train, evaluate, apply and visualize models. AVAILABILITY AND IMPLEMENTATION: CNN-PepPred is freely available as a Python tool with a detailed User’s Guide at https://github.com/ComputBiol-IBB/CNN-PepPred. The site includes the peptide sets used in this study, extracted from IEDB (www.iedb.org). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.