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PickPocket 1.1 Server

PickPocket server predicts binding of peptides to any known MHC molecule using positiion specific weight matrices. The method is trained on more than 150,000 quantitative binding data covering more than 150 different MHC molecules. Predictions can be made for HLA-A, B, C, E and G alleles, as well as for non-human primates, mouse, Cattle and pig. Further, the user can upload full length MHC protein sequences, and have the server predict MHC restricted peptides from any given protein of interest.

Version 1.1 has been retrained on extented data set including 10 prevalent HLA-C and 7 prevalent BoLA MHC-I molecules.

The PSWM's are generated using the SMM_pmbec method described in 19948066

Predictions can be made for 8-12 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, IMMI, and LIAI.

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

Link to table (tab seperated) describing the training data Training data table

As of July 8th, the nomenclature for BoLA-I has been updated to follow IPD Release 1.3.

Instructions Output format Article abstract


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 allele names (ie HLA-A01:01) separated by commas (and no spaces). Max 20 alleles per submission)

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

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

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

Sort by affinity 

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:

The PickPocket method for predicting binding specificities for receptors based on receptor pocket similarities: application to MHC-peptide binding
Zhang H, Lund O, Nielsen M. Bioinformatics. 2009 May 15;25(10):1293-9

PMID: 19297351       Full text


Would you prefer to run PickPocket at your own site? PickPocket v. 1.1 is available as a stand-alone software package, with the same functionality as the service above. Ready-to-ship packages exist for Linux and Darwin (MacOSX). There is a download page for academic users; other users are requested to contact CBS Software Package Manager at


Scientific problems:        Technical problems: