NetMHCIIpan 3.0 server predicts binding of peptides to MHC class II molecules. The predictions are available for all three human MHC class II isotypes, HLA-DR, HLA-DP and HLA-DQ, as well as mouse molecules. NetMHCIIpan 3.0 server can produce predictions for peptides of 9 - 19 amino acids in length. 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. For HLA-DP and HLA-DQ molecules alpha and beta chains can be chosen separately from the list. Also, for HLA-DP, HLA-DQ and mouse molecules, full length sequences of alpha and beta chains should be uploaded separately. For HLA-DR only beta chain sequence should be uploaded. 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.

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References in zbMATH (referenced in 1 article )

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  1. Shen, Wen-Jun; Wong, Hau-San; Xiao, Quan-Wu; Guo, Xin; Smale, Stephen: Introduction to the peptide binding problem of computational immunology: new results (2014)

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