intrensic disrodered proteins

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    • April 4, 2019 at 2:20 pm #3107
      Anonymous

        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?

      • April 8, 2019 at 9:49 pm #14651
        Anonymous

          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

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