On Wed, Feb 20, 2013 at 12:39 PM, Jacob Keller <j-kell...@fsm.northwestern.edu> wrote: > it has been my experience that homology modelling programs get folds pretty > well, but sometimes the details are pretty obviously bad, like too-close > contacts. One might think that the modelling software would put in a sort of > "polishing" step, but they don't seem to. Is there any way to trick the CCP4 > or other software to fix these things, such as by simulated annealing or > otherwise, I guess without any weight on the [non-existent] structure > factors?
What software were you using? There must be dozens of papers (at least) on this subject, and assessment of refinement and model quality is a major part of the CASP competition. The Rosetta "relax" protocol is one of the best known, but there are many other approaches (including MD), some of which are definitely integrated into modeling pipelines. I'd start here: https://www.rosettacommons.org/manuals/archive/rosetta3.4_user_guide/d6/d41/relax_commands.html and also: https://www.rosettacommons.org/manuals/archive/rosetta3.4_user_guide/d5/d4e/comparative_modeling.html Of course if the model is too awful, there isn't much that can be done to relieve gross errors without completely rebuilding. I don't know what the radius of convergence of the various protocols is; Rosetta relax certainly can't fix some of the truly awful models in the PDB (but it's by no means the only option). -Nat
