You are here

ddg monomer vs pmut scan

4 posts / 0 new
Last post
ddg monomer vs pmut scan
#1

Hello,

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?

Dave

Post Situation: 
Tue, 2014-03-04 10:18
dave

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).

Tue, 2014-03-04 10:28
smlewis

thanks, ddg_monomer works really well. But pmut_scan looks also usefull for some basic analysis. Is it possible to output all energy values (and not only those predicted as stabilizing)?

Fri, 2014-03-07 12:16
dave

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).

Fri, 2014-03-07 13:02
smlewis