NetMHCIIpan 3.1 Server
NetMHCIIpan 3.1 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 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.
Refer to the instructions page for more details.
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:
Accurate pan-specific prediction of peptide-MHC class II binding affinity with improved binding core identification
and Nielsen M
Benchmark data used to develop this server were obtained from:
Would you prefer to run NetMHCIIpan at your own site? NetMHCIIpan 3.1 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. There is a
for academic users; other users are requested to contact CBS Software Package
Manager at firstname.lastname@example.org.