script recommendations? for high res docking from low res

[Anonymous]

Hi:

Is there a rosetta or pyrosetta script  (or general protocol) you would recommend for a pdb that already has a small molecule ligand docked in a low resolution docking model?

I used Zhang lab’s BP Slim server to get this lo res docking, and now what I need to do is refine that model to high res, atomic scale.

 

thank you all so much, I am learning rapidly from this most generous and helpful community.  – Amy

[Anonymous]

just to test, I am running my ligand docked pdb on this server

 

http://flexpepdock.furmanlab.cs.huji.ac.il/usage.php

anyone used this?

 

see how that goes… ‘-)  Amy

[Anonymous]

well it did not go well

 

Unfortunately, we noticed your job [id: 15375, name: 81q1_eru_dock.pdb] failed with the following error message:

PDB file format error: Please use a pdb file with exactly 2 chains.

 

[Anonymous]

The standard Rosetta small molecule docking protocols are typically split into low-res and high-res stages.

If you use the RosettaScripts protocol (e.g. https://www.rosettacommons.org/demos/latest/tutorials/ligand_docking/ligand_docking_tutorial) you can simply disable/remove the “Transform” mover from the XML to disable the low resolution sampling stage. You can also change the settings on the Transform mover to be less agressive about how it samples.

If you’re using PyRosetta, it should be relatively straightforward to translate the XML into a PyRosetta script. Alternatively, I think the D120_Ligand_interface.py does primarily a high resolution refinement. (Though it may be more agressive than the without-Transform mover.)

 

The flexpepdock protocol (and server) is intended for docking peptides, so it’s not going to work well for non-peptidic small molecules.

[Author]

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