Hello Rosetta Users,
I am new to Rosetta. I am trying to preprocess input structures for interface design using the relax application. While playing around with various options, I noticed that the default relax run using an -nstruct 50 produces structures that on superposition seem to resemble an ensemble of structures, similar to something we would obtain from NMR experiments. Futhermore, I noticed that running relax on protein structures that are known to be stable produce an ensemble with low fluctuations around the mean positions, whereas more flexible proteins have high fluctuations around the mean positions.
Since the next step in my workflow involves ensemble docking with another protein partner, it occured to me that these ensembles for both protein partners (as obtained from relax step) can be used for docking and producing all combinations of protein-protein complexes. Is this the right way to go about it? Alternatively, I was thinking of generating the ensemble using CONCOORD, but that would involve addtional steps and extra amount of work to parse and prepare the output for the docking and design step. Using Relax seemed to be a simpler approach, but is it a correct one?
Thanks in advance.