I have been running several fixbb and flxbb protocols for a while now, but it seems the outcome is not very promising.
So i guess mainly the issue is with disordered structures? Whatever I RosettaDesign i always end up with decoys that have intrensic disrodered states for the majority of the residues in a structure.
this of course affect the folding simulation to determine the success of the design, as well as the crystallisability of the structure.
My question is: how can I overcome this issue? how can i push Rosetta to sequence design (fixbb or flxbb) and reduce the probability of ending up with intrinsically disordered proteins?