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NetMHCIIpan 3.0 Server

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.


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 reference.

Instructions Output format Article abstract Data sets

SUBMISSION

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 species/loci


Select Allele (max. 20 per submission)


or type molecules names (e.g. DRB1_1121 or HLA-DQA10511-DQB10404) separated by commas (and no spaces). Max. 20 alleles per submission

For the list of allowed molecule names click here: List of MHC molecule names.

or paste a single full length protein sequence of MHC alpha chain in FASTA format into the field below:

or submit a file containing a full length sequence of MHC alpha chain in FASTA format directly from your local disk:


or paste a single full length protein sequence of MHC beta chain in FASTA format into the field below:

or submit a file containing a full length sequence of MHC beta chain in FASTA format directly from your local disk:

Threshold for strong binder (% Rank)  Threshold for strong binder (IC50) 
Threshold for weak binder (% Rank)  Threshold for weak binder (IC50) 

Filter output

Use fast mode (recommended for large calculations) 

Print only the strongest binding core 

Sort output by affinity 

Save predictions to xls file 

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

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


CITATIONS

For publication of results, please cite:

  • NetMHCIIpan-3.0, a common pan-specific MHC class II prediction method including all three human MHC class II isotypes, HLA-DR, HLA-DP and HLA-DQ
    Karosiene E, Rasmussen M, Blicher T, Lund O, Buus S, and Nielsen M
    Immunogenetics, 2013

DATA RESOURCES

Data resources used to develop this server was obtained from


PORTABLE VERSION

No stand-alone version of the NetMHCIIpan-3.0 software is available at the moment. Please contact CBS Software Package Manager at software@cbs.dtu.dk.


GETTING HELP

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