NetMHCII 2.0 Server
NetMHCII 2.0 server predicts binding of peptides
to HLA-DR and mouse MHC class II alleles using articial neuron networks.
Predictions can be obtained for 14 HLA-DR alleles covering the 9 HLA-DR supertypes, and three mouse H2 class II
The predictions are given in nM IC50 values and as a %-Rank to a set of 1000.000 random natural peptides.
Strong and weak binding peptides are indicated in the output.
The server can be run in two modes. Default mode is without P1 amino acids preference. This mode is recommended
for accurate binding affinity prediction. The other mode includes P1 amino acids preference encoding, and
is turned on selecting the Turn of P1 amino acid preference option. This option is recommended for accurate
binding core identification.
View the version history of this server.
All the previous versions are available on line, for comparison and
For publication of results, please cite:
NN-align. A neural network-based alignment algorithm for MHC class II peptide binding prediction.
Nielsen M and Lund O
Prediction of MHC class II binding affinity using SMM-align, a novel stabilization matrix alignment method.
Nielsen M, Lundegaard C, Lund O.
Would you prefer to run NetMHCII at your own site? NetMHCII v. 2.0
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