Rosetta Script for ddg_monomer protocol 16

[Anonymous]

Hi all. 

I want to predict the effect of a point mutation in a protein stability. I have the .pdb crystal structure of the wild type.

After a literature search, I think this paper presents the most comprehensive study of different methods for this analysis DOI:10.1002/prot.22921. So I want to do the prediction using their protocol 16. I also found python code for this protocol here: https://github.com/Kortemme-Lab/ddg/tree/master/protocols/ddg_monomer_16.

My question is if anyone has setup a Rosetta Scripts .xml file to reproduce this protocol?

[Anonymous]

Note that the Kortemme lab scripts you point to aren’t actually running the protocol in PyRosetta, instead they’re job-handling scripts which invoke (though a subshell) the actual ddg_monomer application.

Unfortunately, the mover which forms the core of the Kellogg ddg_monomer protocol is not accessible through RosettaScripts. That said, you should be able to be able to put together a sequence of PackRotamersMovers and MinMovers which approximate the protocol being used by the ddg_monomer application.

The tricky bit would be the constraints which are added by the ddg_monomer application. For minimization, these are Calpha-Calpha distance constraints for all protein residues within 9 Ang. I belive that a close approximation can be obtained with the AddConstraintsToCurrentConformationMover, changing `use_distance_cst` to true, `max_distance` to 9.0 and coord_dev to 0.5.

[Anonymous]

Since the Kellogg et al paper, have there been improvements in using ROSETTA for prediction of stability ddG’s of mutations in single proteins? Is there an updated protocol?

[Author]

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