NetMHCIIpan - 3.2

Pan-specific binding of peptides to MHC class II alleles of known sequence

NetMHCIIpan 3.2 server predicts binding of peptides to MHC class II molecules. The predictions are available for the three human MHC class II isotypes HLA-DR, HLA-DP and HLA-DQ, as well as mouse molecules (H-2).

Submission is accepted in two formats - as a list of peptides or as a protein sequence in FASTA format. A comprehensive list of MHC molecules is available for prediction, alternatively the user can upload their MHC protein sequence of interest.

The prediction values are given in IC50 values (in nanoMolars) and as %Rank. The percentile rank for a peptide is generated by comparing its score against the scores of 200,000 random natural peptides of the same length of the query peptide. For example, if a peptide is assigned a rank of 1%, it means that its predicted affinity is among the top 1% scores for the specified molecule.
Strong and weak binding peptides are identified based on %Rank, with customizable thresholds. You may sort the output based on predicted binding affinity and filter out non-binders.

The project is a collaboration between CBS, IMMI at copenhagen university and LIAI.

NEW: visualize sequence motifs of the molecules in the NetMHCIIpan library with the Motif viewer.


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