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.
I am experiencing the same kind of problem with pose docking. I think I am using correct input with rosetta, but in the end, the backbone is unchanged all the time.
my input is :
rosetta.exe aa myprot 1 -s 1 myprot.ppk -dock -pose -dock_mcm -dock_rtmin -nstruct 10 -fake_native -dock_pert 0 0 0 -ex1 -ex2aro_only -unboundrot -use_score12
and I also tried to add : -pose_loops_file myprot.pose_loops
but nothing happend, except for a normal rigid backbone docking.
do you know what I am doing wrong ?