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mhc-class-ii-prediction

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Predict peptide-MHC class II (HLA-DR/DQ/DP) binding and presentation for CD4 T-cell epitopes with NetMHCIIpan-4.3 and MixMHC2pred-2.0. Covers why class II is far less reliable than class I (open binding groove, 9-mer register ambiguity, sparse noisy training data, DR>DP>DQ accuracy asymmetry), the DQ/DP heterodimer alpha/beta pairing trap, and the looser 1%/5% %Rank thresholds. Use when predicting CD4 epitopes for vaccine help, mapping class II neoantigens, or scoring long peptides against DR/DQ/DP. For CD8/class I see mhc-binding-prediction.

When to use

• Predicting CD4 epitopes for vaccine help
• Mapping class II neoantigens
• Scoring long peptides against DR/DQ/DP
• Nominate candidate CD4 T-cell epitopes
• Inferring the 9-mer binding core within long peptides

When not to use

• CD8/class I prediction

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