Thomas Trolle
Denmark
Research Article
Improved Peptide-MHC Class II Interaction Prediction Through Integration of Eluted Ligand and Peptide Affinity Data
Author(s): Christian Garde, Ramarathinam H, Emma C Jappe, Morten Nielsen, Jens V Kringelum, Thomas Trolle and Anthony W PurcellChristian Garde, Ramarathinam H, Emma C Jappe, Morten Nielsen, Jens V Kringelum, Thomas Trolle and Anthony W Purcell
Major histocompatibility complex (MHC) class II antigen presentation is a key component in eliciting a CD4+ T-cell response. Precise prediction of peptide-MHC (pMHC) interactions has thus become a cornerstone in defining epitope candidates for rational vaccine design. Current pMHC prediction tools have, so far, primarily focused on inference from in vitro binding affinity. In the current study, we collate a large set of MHC class II eluted ligands generated by mass spectrometry to guide the prediction of MHC class II antigen presentation. We demonstrate that models developed on eluted ligands outperform those developed on pMHC binding affinity data.
The predictive performance can be further enhanced by combining the eluted ligand and pMHC affinity data in a single prediction model. Furthermore, by including ligand data, the peptide length preference of MHC class II can be accu.. View More»