NetMHCcons 1.0 Server

NetMHCcons 1.0 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.

NetMHCpan is a pan-specific ANN method trained on more than 115,000 quantitative binding data covering more than 120 different MHC molecules.

PickPocket method is matrix-based and relies on receptor-pocket similarities between MHC molecules. It has been trained on 94 different MHC alleles.

NetMHCcons 1.0 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 reference.

Instructions

Output format

Article abstract