[gmx-users] Interaction study for peptide-receptor..
jalemkul at vt.edu
Thu Oct 4 12:27:42 CEST 2012
On 10/4/12 2:01 AM, rama david wrote:
> Hi gromacs Friends,
> I want to do peptide-receptor ( Protein) interaction
> study.Receptor consist a single chain.
> Peptide is made up of 4 amino acids. I know the interaction pattern of
> peptide and receptor.
> I plan to mutate single residue each at a time and run 4 simulation .
> So I will have the 4 different simulation that contain the mutated residues
> and the wild one.
> Then afterward from the interaction energy I want to select the peptide
> which is showing
> stronger interaction than others.
> As mention I know the binding site, If I freeze the remaining portion in
> that not involved in binding , Is it going to affect my screening process
Potentially. Do you know that the binding interactions and the mutations will
only perturb local residues? Do you know that there are no long-range motions
to be considered?
I think you gain very little by freezing portions of the system, and risk more
than you gain.
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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