Does anyone have any experience with flexible backbone docking?
I am attempting to run this protocol using Rosetta 2.3.
I have been following the instructions in the provided documentation, but
they do not lead to the expected result. I am attempting to dock two proteins, where both have flexible backbones. Instead, I find that the first protein is entirely unperturbed.
What is the command line that you are using? Does the second partner undergo any changes in backbone conformation? Or is it just moving in rigid-body position/orientation?
In standard fix-bb docking, the first partner is always entire un-perturbed, but in flexible docking with both partners flexible, the first partner’s backbone conformation should change, if only slightly.