I have a protein and I am only interested in modeling two parts of it, constraining the rest of the protein to the structure that we already know. I am new to Rosetta and would like to know what the best approach to this would be.
I am assuming that homology modeling is the way to go and have studied the tutorial, but without constraining the well defined part of the protein I am afraid that it will be impossible to produce a model that will be of structural significance. Could anyone assist me what the best way to set those constraints would be ( essentially just freezing the parts that we are not interested in modelling but I still want them to be there so that the parts of the protein that I am interested in are linked to the rest of the chain sensibly).
Thank you for any inout in advance