Run MixMHC2pred Predict motifs List alleles Help/FAQ Download MixMHC2pred

Predicting MHC class II ligands (MixMHC2pred-2.0)

Input your peptide sequences in the box below:
(one peptide per line; or if context encoding option from below is selected, a 2nd column gives the 12 AAs from the peptide context (see the help page for details))
Or click here for an example of peptide sequences with context encoding.
Or here for an example of the format used without context encoding.

Name for the results file (it cannot contain spaces or special characters):

Enter the list of MHC-II alleles for which you want to make predictions:
(each allele is separated by a space or a coma;
list of available alleles can be found here; e.g., DRB1_01_01, DPA1_01_03__DPB1_02_01, H2_Aa_b__H2_Ab_b;
or new user-defined alleles should be first predicted from this page)

Optional Motifs run ID for user-defined alleles:

Predicting binding specificities from MHC-II sequences

This section allows predicting motifs describing the binding specifitiy for any MHC-II allele sequence. This part corresponds to the first neural network block from MixMHC2pred (see e.g., Figure 4A from Racle et al. Immunity. 2023).
The results can then be used to predict the presentation of MHC-II ligands and CD4+ T-cell epitopes for these alleles with MixMHC2pred.

Upload the sequences of your MHC-II alleles in the box below:
(it should be a tab-delimited file with a header row and at least 3 columns: Allele (the name of the MHC-II allele), seq.alpha and seq.beta (the alpha and beta chain sequences, respectively); multiple alleles can be listed on separate rows; see the help page for details; an example file is available here)

Or give a list of MHC-II allele names for which you want to predict the motifs:
(each allele is separated by a space or a coma; list of available alleles can be found here)

Retrieving previous results

Motifs run ID from a previous run (these results are kept for about one month on the server):

Uploading previously obtained MHC-II allele definition files

Upload in the box below PWMdef files that were downloaded previously from this page:
(you can either upload a single ".zip" file containing multiple allele definition files or the individual ".txt" files defining each allele)