NetMHCpan 3.0 Server
Prediction of peptide-MHC class I binding using artificial neural networks (ANNs).
View the version history of this server.
All previous versions are available online, for comparison and
NetMHCpan server predicts binding of peptides to any MHC molecule of known sequence using artificial neural networks
(ANNs). The method is trained on more than 180,000 quantitative binding data covering 172 MHC molecules from human (HLA-A, B, C, E),
mouse (H-2), cattle (BoLA), primates (Patr, Mamu, Gogo) and swine (SLA). Furthermore, the user can obtain binding predictions to the any custom MHC class I molecule by uploading a full length MHC protein sequence.
Version 3.0 has been retrained on an extented data set of 8-13mer peptides using the
method described in this paper
Predictions can be made for peptides of any length.
Note that most HLA molecules have a strong preference for binding 9mers.
NEW: As of Oct 26th, an option to display sequence logo representations of the predicted binding motifs
has been included. This option is available in the bar below as "Sequence motifs".
Link to table (tab seperated) describing the training data Training data table
Link to file with training data including partitions from 5 fold cross-validation Training data
The project is a collaboration between CBS, ISIM, and LIAI.
For publication of results, please cite:
NetMHCpan-3.0: improved prediction of binding to MHC class I molecules integrating information from multiple receptor and peptide length data sets
Morten Nielsen and Massimo Andreatta
Genome Medicine (2016): 8:33
NetMHCpan, a method for MHC class I binding prediction beyond humans
Ilka Hoof, Bjoern Peters, John Sidney, Lasse Eggers Pedersen, Ole Lund, Soren Buus, and Morten Nielsen
Immunogenetics 61.1 (2009): 1-13
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),
- HLA protein sequences were obtained from the IMGT/HLA database (version 3.1.0).
Would you prefer to run NetMHCpan at your own site? NetMHCpan v. 3.0
is available as a stand-alone software package, with the same
functionality as the service above. Ready-to-ship packages
exist for the most common UNIX platforms. There is a
for academic users; other users are requested to contact
CBS Software Package Manager at