NetMHCcons 1.1 Server
NetMHCcons 1.1 server predicts binding of peptides to any known MHC class I molecule. This is a consensus method for MHC class I predictions
integrating three state-of-the-art methods NetMHC, NetMHCpan and PickPocket to give the most accurate predictions. The server also allows to use
each of these methods separately:
NetMHC is an artificial neural network-based (ANN) allele-specific method which has been trained using 94 MHC class I alleles. Version 3.4 is used as part of NetMHCcons-1.1.
NetMHCpan is a pan-specific ANN method trained on more than 115,000 quantitative binding data covering more than 120 different MHC molecules. Version 2.8 is used as part of NetMHCcons-1.1.
PickPocket method is matrix-based and relies on receptor-pocket similarities between MHC molecules. It has been trained on 94 different MHC alleles. In the PickPocket version 1.1, the matrices of pocket-library are
generated using the SMMPMBEC method.
NetMHCcons 1.1 server can produce predictions for peptides of 8-15 amino acids in length. It also gives a possibility to choose several lengths.
Two submission types are handled - the list of peptides or a protein sequence in FASTA format. The server provides a possibility for the user to
choose MHC molecule in question from a long list of alleles or alternatively upload the MHC protein sequence of interest.
The prediction values are given in nM IC50 values and as % Rank to a set of 200.000 random natural peptides. The user has a choice of setting the threshold for defining strong and
weak binders based on predicted affinity (IC50) or % Rank. Strong and weak binding peptides will be indicated in the output. The output can also be sorted based on predicted
binding affinity as well as filtered on the user-specified thresholds.
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
For publication of results, please cite:
NetMHCcons: a consensus method for the major histocompatibility complex class I predictions
Edita Karosiene, Claus Lundegaard, Ole Lund and Morten Nielsen
Data resources used to develop this server was obtained from
- IEDB database.
- Quantitative peptide binding data were obtained
from the IEDB database.
No stand-alone version of the NetMHCcons software is available at the
CBS Software Package Manager at