How to improve ROSIE docking2 results?

What you’re looking for in a docking output is to have a “funnel like” score-vs-rmsd plot. This means that both the score and the rmsd for the most “native like” structure is low, and as you get higher in rmsd you get higher in energy. The higher you get, the “more stable” Rosetta thinks the native conformation is, but even with benchmark cases this isn’t necessarily a really big difference. Also, the place where you start to plateau doesn’t matter all that much. The main thing you’re looking for is to avoid dips in the score-vs-rmsd plot at higher rmsd, which indicate there might be an alternative conformation which also docks well. (But keep in mind which structure is the reference for the rmsd plot – you may need to redock/recalculate the rmsd using a different structure as your “native” reference structure.) Additionally, it’s really the bottom edge of the funnel plot that you’re looking at – it’s expected that there will be higher energy structures with low rmsd. The Rosetta energy function is rugged, and it doesn’t take much structural change to get a large change in energy.

The “knobs” you have available to you on ROSIE are rather limited. If you were using the full version of Rosetta, I would suggest supplementing the docking runs with constraints derived from experimental data, information from homologs, and your own biological intuition. However, ROSIE docking isn’t set up for that sort of runs. (As there are too many variables to give a good generalized protocol.)

I’m not entirely sure on what you’re hoping to achieve with the output structure, so it’s hard to give a complete analysis of what sort of things you might want to try. (e.g. things you might want to try could vary based on if you are looking to design an interaction

One possibility is to start with alternate starting structures. Slightly different backbone conformations can sometimes result in better docking output. (For example, if a loop conformation is important to the docking interaction, using a different conformation of that loop could give better docking results.) If you had the regular Rosetta release, I might recommend running a relax on the two monomers to generate slightly different conformations of the structures. If you have other version of the starting structures (e.g. other crystallized forms, different chains in the same crystal, etc.) you may want to try docking with them instead.

Another possibility is that the interface you’re looking at isn’t really the true docking interface. Using the local_docking protocol, you may want to start the two partners with a different interface which might be a better interaction site.

I don’t think repeatedly cycling docking results will get you much. The one place where it might is if the docking runs give you alternative minima. Redocking with the alternative minima might find better results in that area. But the sampling should be efficient enough that close output structures (e.g. within 1-2 Ang rmsd to the input structure) won’t gain you much extra by resampling them.

For symmetric docking, you’re basically limited to changing the input monomer backbone structure. All other parameters are set by the type of symmetry you have. It will only take in a monomer – ROSIE isn’t set up to refine a symmetric multimer, although that is something that’s possible with regular Rosetta.