NetMHCpan 4.0 Server
Prediction of peptide-MHC class I binding using artificial neural networks (ANNs).
New in this version: the method is trained on naturally eluted ligands AND on binding affinity data.
It returns two properties: either the likelihood of a peptide becoming a natural ligands, or the predicted binding affinity.
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 a combinatino of more than 180,000 quantitative binding data and MS derived MHC eluted ligands. The binding affinity data covers 172 MHC molecules from human (HLA-A, B, C, E),
mouse (H-2), cattle (BoLA), primates (Patr, Mamu, Gogo) and swine (SLA). The MS eluted ligand data covers 55 HLA and mouse allelee. Furthermore, the user can obtain redictions to the any custom MHC class I molecule by uploading a full length MHC protein sequence.
Predictions can be made for peptides of any length.
11-03-2019: Server updated to have precalculated percentile rank values and binding motifs for all HLA alleles included in the latest IMGT HLA release
The project is a collaboration between CBS, ISIM, and LIAI.
For publication of results, please cite:
NetMHCpan-4.0: Improved Peptide–MHC Class I Interaction Predictions Integrating Eluted Ligand and Peptide Binding Affinity Data
Vanessa Jurtz, Sinu Paul, Massimo Andreatta, Paolo Marcatili, Bjoern Peters and Morten Nielsen
The Journal of Immunology (2017) ji1700893; DOI: 10.4049/jimmunol.1700893
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. 4.0
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