Dear All,
I would like to simultaneously dock and design two (or more) identical subunits into a a symmetric homooligomer.
Input:
- backbone structure of a monomer (no sidechains!);
- initial arrangement of the subunits;
- constraints that precisely define interactions between the subunits.
Simulation:
- simulation must allow for the backbone flexibility (fulfilling the constrains will require deformation of the input backbone, but the secondary structure won't change);
- during the simulation interface and non-interface side chains should be designed.
Perhaps alternating constrained symmetric relaxation and symmetric design would do the job?
I would appreciate any hints on this problem (e.g. RosettaScripts examples)
Best wishes,
Staszek
The first place I'd probably start for symetric docking and design is the symetric protein cage papers coming out of the Baker lab. (e.g. http://dx.doi.org/10.1126/science.1219364 http://dx.doi.org/10.1038/nature13404 http://dx.doi.org/10.1038/nature18010 http://dx.doi.org/10.1126/science.aaf8818 ) You might not need the same scale of symmetry, but the principles and approach should be the same.
The other suggestion would be to take a look at the Protein Design tutorial, which actually does design on a symmetric protein. It doesn't do symmetric docking, but we also have a Symmetric Docking tutorial that may be of interest.
Feel free to ask additional questions, if there's details you're not getting, or wondering how to adjust certain protocols to your system.