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.
Until now the templates that I used had a high sequence identity with the target, but now I have cases where the identity is 3 out 9 or even less.
My question regarding this is:
Does it make sense to still use templates when they are so different to the target and, if so, what kind of modelling protocol would be an option for those cases (ab initio, KIC fragments, hybridizing multiple templates)?
Thank you in advance.