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.
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.
View the version history of this server. All the previous versions are available on line, for comparison and reference.
For publication of results, please cite:
Other relevant publications:
Data resources used to develop this server was obtained from
Would you prefer to run NetMHCcons at your own site? NetMHCcons v. 1.1
is also available as a stand-alone software package with the same
functionality as the service above.
exist for Linux and Darwin (MacOSX). There is a
for academic users; other users are requested to contact
Scientific problems: Technical problems: