How to minimize only a few key residues’ orientation

[Anonymous]

Hi everyone,

I am currently checking mutations of some key residues in the substrate binding pocket. So far, I used pymol wizard to automatically iterate all 20 amino aicds mutations from position and then use rosetta minimizer to optimize the local energy. 

Since I only change a few residues of the protein, is there any ways that I can only minimize a few positions instead of minimization of whole protein?

 

Thanks,

Ronghai

[Anonymous]

Generally, you would want to use a MoveMapFactory (or MoveMap) to select the residues of interest, pass that to to the MinMover, and use cartesian miminimization and a cartesian scorefxn. https://www.rosettacommons.org/docs/latest/scripting_documentation/RosettaScripts/RosettaScripts#rosettascript-sections_move_map_factories

 You would need to do this via RosettaScripts OR PyRosetta.  If you don’t set the MinMover to use cartesian, you will get downstream movement.  https://www.rosettacommons.org/docs/latest/scripting_documentation/RosettaScripts/xsd/mover_MinMover_type

This script I wrote gives an example of this: https://github.com/SchiefLab/Jade/blob/master/database/rosetta/xml_scripts/design_focus_basic.xml

Here, it basically miminizes the ‘focus’ – IE the design residues, while packing the surrounding residues – ‘nbrhood’ in FastRelax. It has a few SimpleMetrics to report energetic changes between this.  In this script, I then design the focus in the same way.  https://www.rosettacommons.org/docs/latest/scripting_documentation/RosettaScripts/RosettaScripts#rosettascript-sections_simple_metrics

The idea is that I do the same minimization to the input as the design – so the energetic differences are more correct – IE NOT artifacts from the minimization.  Hope this helps to give you a starting point. 

-Jared

[Anonymous]

Hi Jared,

I am so appreciate for your help! I will try your method right away and give the update for you soon.

 

Ronghai

[Author]

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