I have a protein dimer and I have to insert amino acid rsidues in both monomer
at same palce. Is it possible to do with Modller without affecting interaction
between protein in crystal structure?
Sure, that should be straightforward (whether it affects the interaction
depends on how big the insertion is and how close it is to the
interface). Just use your original dimer as the template and build a
model using an alignment that looks something like
template AAAAA--AAAAA/AAAAA--AAAAA*
model AAAAABBAAAAA/AAAAABBAAAAA*
where A represents the original sequence of your dimer, / the chain
break, and B the inserted residues.