Change MHCII peptide length

[ohyesweilun]

Thanks for sharing the great work.

I am wondering if there is a simple way to change or vary MHCII peptide length? It seems the length is fixed to 11 aa in the codes. Many thanks!

[phbradley]

Hi Grace, thanks for your interest! Unfortunately, TCRdock requires you to break the peptide into overlapping windows of length 11 and run the model on all those, taking the prediction with the best confidence score; or try predicting the core 9-residue segment using a class II peptide-MHC predictor (like netmhc2pan) and then add one residue on either side. This is because TCRdock modeling requires an alignment between the target peptide and the template peptides in solved class II pMHC structures. Those template structures have all been parsed ahead of time to define just the core 9 residue peptide window (plus one AA on either side) during the template database setup.