NetMHCII 2.0 Server

NetMHCII 2.0 server predicts binding of peptides to HLA-DR and mouse MHC class II alleles using articial neuron networks.

Predictions can be obtained for 14 HLA-DR alleles covering the 9 HLA-DR supertypes, and three mouse H2 class II alleles.

The predictions are given in nM IC50 values and as a %-Rank to a set of 1000.000 random natural peptides. Strong and weak binding peptides are indicated in the output.

The server can be run in two modes. Default mode is without P1 amino acids preference. This mode is recommended for accurate binding affinity prediction. The other mode includes P1 amino acids preference encoding, and is turned on selecting the Turn of P1 amino acid preference option. This option is recommended for accurate binding core identification.

View the version history of this server. All the previous versions are available on line, for comparison and reference.

Instructions Output format Article abstract Training and Evaluation Data


Paste a single sequence or several sequences in FASTA format into the field below:

Submit a file in FASTA format directly from your local disk:

MHC Allele (use ctrl key to select multiple alleles)        

Threshold         Peptide length         Sort by affinity 
Turn of P1 amino acid preference 

At most 5000 sequences per submission; each sequence not more than 20,000 amino acids and not less than 9 amino acids.

The sequences are kept confidential and will be deleted after processing.


For publication of results, please cite:

  • NN-align. A neural network-based alignment algorithm for MHC class II peptide binding prediction.
    Nielsen M and Lund O
    PMID: 19765293
    Full text
  • Prediction of MHC class II binding affinity using SMM-align, a novel stabilization matrix alignment method.
    Nielsen M, Lundegaard C, Lund O.
    PMID: 17608956
    Full text


Would you prefer to run NetMHCII at your own site? NetMHCII v. 2.0 is available as a stand-alone software package, with the same functionality as the service above. Ready-to-ship packages exist for the most common UNIX platforms. There is a download page for academic users; other users are requested to contact CBS Software Package Manager at


Scientific problems:        Technical problems: