NetMHCII 2.1 Server NetMHCII 2.1 server predicts binding of peptides to HLA-DR, HLA-DQ, HLA-DP 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, four HLA-DQ, four HLA-DP, and three mouse H2 class II alleles. The prediction values 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 with P1 amino acids preference. This option is recommended for accurate binding core identification. The other mode excludes P1 amino acids preference encoding, and is turned on selecting the Turn of P1 amino acid preference option. This mode is recommended for accurate binding affinity prediction. View the version history of this server. All the previous versions are available on line, for comparison and reference.

 

Instructions

Output format

Article abstract

Training and Evaluation Data

CITATIONS

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
  PMID: 19765293
  Full text
• Prediction of MHC class II binding affinity using SMM-align, a novel stabilization matrix alignment method.
  Nielsen M, Lundegaard C, Lund O.
  PMID: 17608956
  Full text

PORTABLE VERSION

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 download page for academic users; other users are requested to contact CBS Software Package Manager at software@cbs.dtu.dk.

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