I am using rosetta for modelling the peptide from a pMHC complex. I have been using a template which I thread into the target sequence which I use in a loop modelling protocol.
When modelling I only focus on the peptide without letting any part of the MHC move, but in some cases, I have bad modelling results.
I was wondering if including the residues of the MHC in contact with peptides in the modelling will be a way to improve the results I am getting.
In case this could be a way of improving the protocol, how should I include these residues in the modelling?
Thank you in advance.