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Pose Docking

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Pose Docking


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.

Sat, 2009-08-08 12:50

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.

- Sid

Tue, 2009-09-01 14:11


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 ?

Thu, 2009-12-10 05:53