Prediction of HLA-DQ3.2{beta} Ligands: evidence of multiple registers in class II binding peptides

Motivation: While processing of MHC class II antigens for presentation to helper T-cells is essential for normal immune response, it is also implicated in the pathogenesis of autoimmune disorders and hypersensitivity reactions. Sequence-based computational techniques for predicting HLA-DQ binding peptides have encountered limited success, with few prediction techniques developed using three-dimensional models. Methods: We describe a structure-based prediction model for modeling peptide-DQ3.2β</it> complexes. We have developed a rapid and accurate protocol for docking candidate peptides into the DQ3.2β</it> receptor and a scoring function to discriminate binders from the background. The scoring function was rigorously trained, tested and validated using experimentally verified DQ3.2β</it> binding and non-binding peptides obtained from biochemical and functional studies. Results: Our model predicts DQ3.2β</it> binding peptides with high accuracy [area under the receiver operating characteristic (ROC) curve A</it><inf>ROC</inf> > 0.90], compared with experimental data. We investigated the binding patterns of DQ3.2β</it> peptides and illustrate that several registers exist within a candidate binding peptide. Further analysis reveals that peptides with multiple registers occur predominantly for high-affinity binders. Contact: <inter-ref locator="shoba@els.mq.edu.au" locator-type="email">shoba@els.mq.edu.au</inter-ref> Supplementary information: Supplementary data is available at Bioinformatics</it> online.