TCR-Pred: A new web-application for prediction of epitope and MHC specificity for CDR3 TCR sequences using molecular...

The search for the relationships between CDR3 TCR sequences and epitopes or MHC types is a challenging task in modern immunology. We propose a new approach to develop the classification models of structure-activity relationships (SAR) using molecular fragment descriptors MNA (Multilevel Neighbourhoods of Atoms) to represent CDR3 TCR sequences and the naïve Bayes classifier algorithm. We have created the freely available TCR-Pred web application (http://way2drug.com/TCR-pred/) to predict the interactions between α chain CDR3 TCR sequences and 116 epitopes or 25 MHC types, as well as the interactions between β chain CDR3 TCR sequences and 202 epitopes or 28 MHC types. The TCR-Pred web application is based on the data (more 250 000 unique CDR3 TCR sequences) from VDJdb, McPAS-TCR, and IEDB databases and the proposed approach. The average AUC values of the prediction accuracy calculated using a 20-fold cross-validation procedure varies from 0.857 to 0.884. The created web application may be useful in studies related with T-cell profiling based on CDR3 TCR sequences.