NetMHCIIpan 3.0 Server
NetMHCIIpan 3.0 server predicts binding of peptides to MHC class II molecules. The predictions are available for all three human MHC class II isotypes, HLA-DR, HLA-DP and HLA-DQ, as well as mouse molecules.
NetMHCIIpan 3.0 server can produce predictions for peptides of 9 - 19 amino acids in length.
Two submission types are handled - the list of peptides or a protein sequence in FASTA format. The server provides a possibility for the user to
choose MHC molecule in question from a long list of alleles or alternatively upload the MHC protein sequence of interest.
For HLA-DP and HLA-DQ molecules alpha and beta chains can be chosen separately from the list. Also, for HLA-DP, HLA-DQ and mouse molecules, full length sequences of alpha and beta chains should be uploaded separately. For HLA-DR only beta chain sequence should be uploaded.
The prediction values are given in nM IC50 values and as % Rank to a set of 200.000 random natural peptides. The user has a choice of setting the threshold for defining strong and
weak binders based on predicted affinity (IC50) or % Rank. Strong and weak binding peptides will be indicated in the output. The output can also be sorted based on predicted
binding affinity as well as filtered on the user-specified thresholds.
The project is a collaboration between CBS, IMMI, and LIAI.
View the version history of this server.
All the previous versions are available on line, for comparison and
For publication of results, please cite:
NetMHCIIpan-3.0, a common pan-specific MHC class II prediction method including all three human MHC class II isotypes, HLA-DR, HLA-DP and HLA-DQ
and Nielsen M
Data resources used to develop this server was obtained from
No stand-alone version of the NetMHCIIpan-3.0 software is available at the
CBS Software Package Manager at