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
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
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.
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
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
for academic users; other users are requested to contact
CBS Software Package Manager at