symmetric design without symmetrizing the structure

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    • September 13, 2016 at 12:49 pm #2510
      Anonymous

        Hello,

        Is it possible to design an homooligomer (each subunit should have the same sequence), but without imposing symmetry on the input structure?

        Best wishes,

        sdh

         

      • September 13, 2016 at 2:41 pm #11858
        Anonymous

          Yes, it should be possible with RosettaScripts, using the FavorSymmetricSequence mover.

          The only requirement on the input structure is that there needs to be an equal number of residues in each symmetric subunit, and they need to be contiguous in the pose you’re working with. (E.g. if you have a (symmetric) trimer of heterodimers, it needs to be layed out A1-B1-A2-B2-A3-B3 and not A1-A2-A3-B1-B2-B3 .)

          Also keep in mind you need to have the “res_type_constraint” term turned on in the scorefunction you’re using for design. You can do this by either using a weights file which has the term turned on (e.g. “talaris2014_cst”), or you can use the “Reweight” subtag in the SCOREFUNCTIONS subsection.

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