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