From: Jason Swails <>
Date: Fri, 24 Jan 2014 16:05:05 -0500

On Fri, 2014-01-24 at 14:24 -0500, bharat lakhani wrote:
> Hi all
> Is it possible to do the binding free energy calculation if you mutate WT
> residue to all possible mutation other than ALA. I know we can do ala
> scanning. also supports Glycine scanning. As Carlos says, it is trivial
to perform those mutations due to their lack of side-chain rotamers
(they are the two smallest amino acids).

Anything else you will actually have to perform the mutation and re-run
the simulations. Since proteins pack fairly densely, it is unlikely
that in-place mutations (like what is done with alanine and glycine)
will yield even qualitatively useful results, so no effort has been put
into enabling such mutations.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Fri Jan 24 2014 - 13:30:03 PST
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