Hi, does anyone know how to do alanine scanning for just one protein?
I looked at different movers for RosettaScripts, like ddgScan, AlaScan, and ddg. Can any of these be used for a single protein with no interface? I want to see which protein residues are good targets for mutation.
The ddg_monomer (Kellogg et al. https://doi.org/10.1002/prot.22921) and cartesian_ddg (Park et al. https://doi.org/10.1021/acs.jctc.6b00819) applications are designed to determine the effect of mutations on monomeric proteins. While not specifically tailored to alanine scanning, they should be able to work with arbitrary mutations, and have been benchmarked/optimized against alanine scanning data (as that’s what most of the experimental mutational data is.)
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