Robust Quantitative Modeling of Peptide Binding Affinities for MHC Molecules Using Physical-Chemical Descriptors

Major histocompatibility complex (MHC) molecules bind short peptides resulting from intracellular processing of foreign and self proteins, and present them on the cell surface for recognition by T-cell receptors. We propose a new robust approach to quantitatively model the binding affinities of MHC molecules by quantitative structure-activity relationships (QSAR) that use the physical-chemical amino acid descriptors E1-E5. These QSAR models are robust, sequencebased, and can be used as a fast and reliable filter to predict the MHC binding affinity for large protein databases.