NetMHCIIpan 3.0 Server
NOTE: The method was updated on 10-11-2014 due to a bug being fixed. The bug affected the results only if the method was used with a PEPTIDE format input file containing peptides of the length other than 15 amino acids. Only in such input case and only the %Rank score (not the IC50 affinity values) were affected by the bug. If you used NetMHCIIpan-3.0 for such specific cases as mentioned above, we suggest to rerun your predictions.
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.
View the version history of this server. All the previous versions are available on line, for comparison and reference.
For publication of results, please cite:
Data resources used to develop this server was obtained from
Would you prefer to run NetMHCIIpan at your own site? NetMHCIIpan 3.0 is available as a stand-alone software package, with the same functionality as the service above. Ready-to-ship packages exist for Linux and MacOSX.
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