[gmx-users] Interaction study for peptide-receptor..

Justin Lemkul 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
> receptor
> 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.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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