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

[Justin Lemkul]

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

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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