I’d like to predict effect of a mutation on a protein stability. I found two different applications – ddg monomer and pmut scan and I’d like to ask what is the difference between them? Are there any applications where one of them is better to use?
ddg_monomer is the better choice here as it does basically what you want. pmut_scan is meant for brute-force, broad exploration of mutation-space to generate footholds for new designs, and is a fair bit less rigorous (to trade for speed).
Use the -DDG_cutoff flag, and pass an absurdly large positive value, like -DDG_cutoff 1000000000000. This will effectively disable the filtering by printing all mutations that have DDGs less than a trillion (which is either all of them, of all of them except a few super huge clashes).