what is the best protein design program that can assess the effect of mutation in a globular protein structure? i am looking to change the specificity of a protein. but mostly i am interested to measure the outcomes of the mutation on the protein itself rather than the interaction. and if i want to look into the interaction as well should i use protein design or MD softwares?
Hi Neda
You can use Pymol software. That is very comfortable software in order to mutate a protein.
One can use Pymol or Modeller to model the mutant protein. But final analysis or the effect of mutation can be understood only after performing some MD-run. GROMACS, NAMD are good tools for carrying out MD, charmm36 being a suitable force-field for protein simulations.
If you want to assess the effects of point mutations on the stability of proteins and protein-protein interfaces, I would use ddG prediction methods. Many of these are available as Web servers, although usually local installation offer better control
https://www.google.ch/search?client=safari&rls=en&q=foldx&ie=UTF-8&oe=UTF-8&gfe_rd=cr&ei=oFKgV-PYHuSX8QeWyoCQAw#q=ddg+prediction+web+server
e.g. rosetta ddG https://www.rosettacommons.org/manuals/rosetta3.1_user_guide/app_ddg_prediction.html
Are you looking for :
I often use the SDM server (http://mordred.bioc.cam.ac.uk/~sdm/sdm_theory.php) for a quick estimate of a mutation impact on a protein structure, maybe it can solve your problem.
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