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NetMHCpan 1.1 Server

NetMHCpan server predicts binding of peptides to 478 and 791 different HLA A and B alleles using artificial neural networks (ANNs). This is a beta version of the server, and it is in the process of being updated with other features (prediction of user defined MHC molecules, ect)

Predictions can be made for 8-11 mer peptides. Note that all non 9mer predictions are made using approximations. Most HLA molecules have a strong preference for binding 9mers.

The prediction values are given in nM IC50 values.

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


Paste a single sequence or several sequences in FASTA or PEPTIDE 9mer (if PEPTIDE 9mer format click the box below) format into the field below:

Submit a file in FASTA or PEPTIDE 9mer (if PEPTIDE 9mer format click the box below) format directly from your local disk:

Click if input is PEPTIDES (NOTE Peptides MUST be of equal length)  

Allele (use ctrl key to select multiple alleles)  

or type allele names (ie A0101) seperated by commas  

Peptide length 

Threshold for presentation         Sort by affinity 

Save prediction to xls file 

At most 5000 sequences per submission; each sequence not more than 20,000 amino acids and not less than 8 amino acids.

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


For publication of results, please cite:

  • NetMHCpan, a Method for Quantitative Predictions of Peptide Binding to Any HLA-A and -B Locus Protein of Known Sequence.
    Nielsen M, et al. (2007) PLoS ONE 2(8): e796. doi:10.1371/journal.pone.0000796 View the abstract, the full text version at PLoSONE: Full text, or Full text including supplementary materials: PDF_fulltext.pdf


Data resources used to develop this server was obtained from

  • IEDB database.
    • Quantitative peptide binding data were obtained from the IEDB database.
  • IMGT/HLA database. Robinson J, Malik A, Parham P, Bodmer JG, Marsh SGE: IMGT/HLA - a sequence database for the human major histocompatibility complex. Tissue Antigens (2000), 55:280-287.
    • HLA protein sequences were obtained from the IMGT/HLA database (version 2.17.0).


Would you prefer to run NetMHC:locifer at your own site? The NetMHC:locifer package is in preparation. It will soon be available for the most common UNIX platforms including MIPS (under IRIX, Silicon Graphics), SPARC (under Solaris, Sun), Alpha (under OSF1) and Pentium family (under Linux). Send inquiries by e-mail to


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