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HLArestrictor 1.2 Server

HLArestrictor is a tool for patient-specific predictions of HLA restriction elements and optimal epitopes within peptides. Given the high-resolution (i.e. 4-digit) HLA typing of the individual, HLArestrictor predicts all 8-11mer peptide-binders within one or more larger peptides and provides an overview of the predicted HLA restrictions and minimal epitopes.

The HLArestrictor-1.2 has been update to the more recent NetMHCpan-2.4 method for peptide MHC binding predictions.

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.

NOTE - if you submit a large job with running time exceeding 10 hours, please use the HLrrestrictor Heavy Queue submission page. There jobs are allowed to run for up to 4 days.

Instructions Output format Article abstract


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:

Select allele subtype (species)

Select Allele (max 20 per submission)

or type host allele names (ie HLA-A01:01) separated by commas.

For list of allowed allele names click here List of MHC allele names.

Peptide length 

Sort mode: 

Sort method

Sort predictions based on %rank score. Prediction are labeled Weak binder and Strong binder according to the thresholds defined below. Peptides are labeled Combined binder if %rank is less than the %rank weak binders threshold and the IC50 value (if defined) is stronger than the affinity weak binding threshold.

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

Number of predictions to show per peptide (0:report down to 2 x weak-binding cutoff.  

Show non-binders with a score of factor*weak binding threshold, 1 means no non-binders are shown.  

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.

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


For publication of results, please cite:

HLArestrictor - a tool for patient-specific predictions of HLA restriction elements and optimal epitopes within peptides
Malene Erup Larsen1, Henrik Kloverpris2, Annette Stryhn3, Catherine K. Koofhethile2, Stuart Sims2,
Thumbi Ndung'u4,5, Philip Goulder2, Soren Buus, and Morten Nielsen1 Immunogenetics. 2010 Nov 16. [Epub ahead of print]

1Center for Biological Sequence Analysis, Technical University of Denmark, DK-2800 Lyngby, Denmark
2University of Oxford, Peter Medawar Building for Pathogen Research, South Parks Road, OX1 3SY, Oxford, England
3Laboratory of Experimental Immunology, Faculty of Health Sciences, University of Copenhagen, Denmark
4HIV Pathogenesis Programme, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
5Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Charlestown, MA, 02129, USA



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