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How to estimate the effect of a mutation on the binding energy?

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How to estimate the effect of a mutation on the binding energy?
#1

Given a protein complex, I would like to estimate the effect of a point mutation on the binding energy (ddG). I'd appreciate if anyone could point me to the Rosetta app(s) that I should look into. I'm fairly new to Rosetta.

Thanks!

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Tue, 2011-02-15 08:02
ltrabuco

I've asked around to see if there's a DDG app already present in 3.2.

If not, doing it with fixbb is pretty simple:
1)Get PDBs of the bound complex and each monomer.
2)Calculate dG of binding by packing them separately subtracting their scores AB-A-B.
3)Do 2) again with the mutation in place (via resfile)
4) subtract 3 from 2 and you have ddG.

Tue, 2011-02-15 17:13
smlewis

After consultation, it seems there isn't a released executeable for this; your best bet is the steps I described.

Wed, 2011-02-16 13:06
smlewis

Thank you very much for looking into this! I'm giving your suggestion a try.

Thu, 2011-02-17 01:11
ltrabuco

If that doesn't work for you, there is a script written by Sid Chaudhury to do just that in PyRosetta:
http://www.pyrosetta.org/scripts

Thu, 2011-03-24 11:15
jadolfbr