You are here


4 posts / 0 new
Last post

I am trying to use ddG_monomer in Rosetta 3.5 to examine the structural effects of a single point mutation. Based on experimental data, it appears as if the mutation causes changes to the backbone of the structure. I would like to use the Monte Carlo ensemble method (protocol 20) from Kellogg et al. paper to model these changes but have not been able to locate the ensemble_generator_score12_sidechain_ver2.linuxgccrelease application listed in the supplementary methods section of the paper. Is the backrub application equivalent to ensemble_generator the application? Would the point mutation application on the RosettaBackrub server work as well as the Monte Carlo ensemble method used in the Kellogg et al. paper?

Post Situation: 
Thu, 2014-06-12 09:53

It looks like that application was never released, an oversight that wasn't caught probably because the MC version didn't provide any significant benefits on the test set versus the simpler protocols. I've emailed Liz Kellogg to see if there's some other reason why the application shouldn't be released. I'll let you know the results.

Thu, 2014-06-12 15:32

I appreciate the help. I am trying to model the structural effects induced by an A to E mutation on a buried residue. The procedure given in the ddG-monomer section of the user manual (protocol#16 from the Kellogg paper) does not seem to allow for enough flexibility to accommodate the mutation. The Kellogg et al paper mentions the backbone and sidechain minimization using position specific constraints method (protocol#18) and the Monte Carlo ensemble method (protocol 20) performed slightly better at predicting structural changes from small-to-large, buried mutations like mine.

How can I generate the type of constraint file used in protocol#18?

The supplementary methods sections mentions a make_cst_file.linuxiccrelease application, but I could not locate it in my Rosetta 3.5 release.

Sun, 2014-06-15 22:15

The ensemble_generator_score12_sidechain_ver2 should be available with the next weekly release version (whenever that actually happens).

Regarding the constraints, the script in source/src/apps/public/ddg/ should do the same thing. It uses the log file of the minimization run. See for details.

Wed, 2014-07-02 16:55