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NetMHCIIpan 2.0 Server

NetMHCIIpan server predicts binding of peptides to more than 500 HLA-DR alleles using artificial neural networks (ANNs). The prediction values are given in nM IC50 values and as %-Rank to a set of 200.000 random natural peptides. The project is a collaboration between CBS and IMMI.

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

Instructions Output format Article abstract Data sets


Type of input

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

or submit a file in FASTA format directly from your local disk:

Peptide length  

Select Loci

Select Allele (max 15 per submission) or type allele names (ie DRBX_XXXX) seperated by commas (max 15 per submission)  

Sort by affinity 
Print only strongest binding core 
Threshold for filtering predictions (only predictions greater than the threshold are displayed) 
Save prediction to xls file 

(please be patient, the calculation might take a few minuts)

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:

    NetMHCIIpan-2.0 - Improved pan-specific HLA-DR predictions using a novel concurrent alignment and weight optimization training procedure
    Nielsen M1, Lundegaard C1, Justesen S2, Lund O1, and Buus S2
    Immunome Res. 2010 Nov 13;6(1):9. .

    View the abstract or the full text version at Full text


Would you prefer to run NetMHCIIpan at your own site? NetMHCIIpan 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: