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docking mover(s) in rosetta

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docking mover(s) in rosetta

Hello all

What is the difference between the DockingMover and the DockingProtocolMover? From what I could gather on the rosettascripts webpage, dockingmover allows design while the protocol has no option for design. But is the difference limited to this. Also what does it mean by "post refactoring" docking protocol.



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Mon, 2016-01-25 02:38

This is one of the unfortunate consequences of Rosetta being developed by 100+ people in 20+ labs across 4 continents - there's a bit of redundancy that seeps in, and people can be hesitant to change and consolidate things, in case it breaks someone else's workflow.

The Docking mover was written as part of the protein-protiein interface design protocol, and is thus optimized for design applications. The DockingProtocol mover, however, comes from the RosettaDock protein-protein docking protocol, and is optimized for (non-design) protein-protein docking. The "post refactoring" bit in the documentation refers to the refactoring of the RosettaDock protocol from an earlier (non-RosettaScripts) form into one which is more RosettaScriptable (the refactoring had nothing to do with the Docking mover). 

It actually turns out that "under the hood" the Docking mover normally calls the DockingProtocol mover for the bulk of the functionality. What the Docking mover brings is additional wrapping that allows for design, and also re-sets the sidechains to their input configuration, when possible. (As opposed to pure docking, where you want to optimize the docked conformation with minimial bias from artifacts in the monmer structures, with design you often want to minimize any variations from the starting structure, so explicitly recovering that information is often warranted.) The Docking mover is also symmetry aware and will automatically substitute the SymDockProtocol mover for the DockingProtocol mover, if needed. 

Thu, 2016-02-04 08:56

Hi Rmoretti

Thank you for the detailed response. It was really helpful in selecting the appropriate mover for my design application.


Mon, 2016-02-22 07:50