How to model oligomeric systems

CS-Rosetta can be combined with docking protocols to model protein oligomers [1]. To model such systems, standard CS-Rosetta/RASREC/AutoNOE is used as the first step to model the monomers separately. The modeled monomers are then docked using symmetric docking or fold and dock protocols in Rosetta to capture possible non-interleaved or interleaved topologies respectively.

Step1: Calculation of monomeric units

As per your requirements, you can use either of the following protocols to calculate structures of monomeric units

Tutorial: CS-Rosetta
Tutorial: RASREC
Tutorial: AutoNOE

Step2: Docking monomers calculated using CS-Rosetta


If you are modeling symmetric oligomers with distinct interfaces between the interacting monomers, you need to generate a symmetry file (see here for more details about the symmetry file supported within Rosetta) to perform symmetric docking (see here to learn about symmetric docking)


If you are modeling domain-swapped symmetric oligomers with a more complex interface, you still need to generate a symmetry file. For this case, the Rosetta fold and dock protocol is more suitable (see here to learn about fold and dock).


If you are modeling asymmetric oligomers with either distinct or domain-swapped topologies, we recommend using the asymmetric fold and dock protocol (see here for details about the protocol).

Cases 1 and 2 were carried out in ref [1] to model symmetric oligomers with both non-interleaved and interleaved topologies. See the commands and flags provided in the Supporting Information document of ref [1] to learn about specifics used in modeling such systems.