Computational protocol: Immunodominant T Cell Determinants of Aquaporin-4, the Autoantigen Associated with Neuromyelitis Optica

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Protocol publication

[…] Quantitative binding affinity servers were used to predict MHC II-restricted epitopes of mAQP4 in C57BL/6 (H-2b) and SJL/J (H-2s) mice. Web-based applications used for prediction for murine alleles included MHCPRED (http://www.darrenflower.info/mhcpred/) , , NetMHCII (I-Ab only) (http://www.cbs.dtu.dk/services/NetMHCII/) , IEDB (http://tools.immuneepitope.org/) and MetaMHC (http://www.biokdd.fudan.edu.cn/Service/MetaMHC.html) . MetaSVMp, an algorithm from the MetaMHC application, is a stacked generalization that combines the base predictors for SMM-align and local alignment (LA) kernel , into a support vector machine. The entire murine AQP4 (M1 isoform) sequence was entered for analysis of overlapping 15 amino acid peptides when applicable. Results are given as values of IC50 (50% inhibition concentration) from programs available for quantitative binding prediction, as well as percentile rankings within algorithms. The inverse of these IC50 values (1/IC50) is plotted in parallel with the top 20% of predicted binding peptides for MetaSVMp. […]

Pipeline specifications

Software tools MHCPred, MetaMHC, SMM-align
Databases IEDB
Application Immune system analysis
Organisms Mus musculus
Diseases Autoimmune Diseases, Neuromyelitis Optica