Hello everyone,
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?
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Post Situation:
This is something that we've been grappling with for some time. One thing that you can do is use the aa_composition score term to require regional amino acid compositions more likely to favour folding. (For example, you can select a loop and enforce that there be at least one proline in that loop.)
Documentation on the aa_composition score term is here: https://www.rosettacommons.org/docs/latest/rosetta_basics/scoring/AACompositionEnergy