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mhc-binding-prediction

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Predict peptide-MHC class I binding and natural presentation with MHCflurry, NetMHCpan-4.1, and MixMHCpred to nominate candidate CD8 T-cell epitopes. Covers the binding-affinity (BA) vs eluted-ligand (EL/presentation) distinction, why %Rank beats raw nM for cross-allele work, the MS abundance bias that misranks low-expression neoantigens, allele-coverage inequity, and length bias. Use when scanning a protein or peptide set for class I epitopes, scoring neoantigen candidates, or choosing a binding predictor. For CD4/HLA class II see mhc-class-ii-prediction.

When to use

• scanning a protein or peptide set for class I epitopes
• scoring neoantigen candidates
• choosing a binding predictor
• predicting peptide-MHC class I binding affinity
• predicting natural presentation likelihood
• nominating candidate CD8 epitopes

When not to use

• CD4/HLA class II prediction

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