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

[Justin Lemkul]

On 10/4/12 8:40 AM, rama david wrote:
> Thank you justin and franscisco,
> I have practical data that claim that only a particular residue that is c
> terminal residue  is
> involve in binding.
>    but when I generate the docking data other residues most of the time
> comes to play.
> I know the binding of natural ligand ( peptide ) and the position.
> so I think if I mutate only these residue and simulate the system I will
> get the
> structure that is more active. In natural ligand the C terminal is playing
> important role.
>
>
> With simulation i will find interaction energy.

"Interaction energy" is a very vague term that people often use fairly 
erroneously to justify their findings.  Force fields are not necessarily 
guaranteed to produce anything meaningful from the sum of nonbonded terms.

>    That will tell me about binding affinity  ( Hope so )

More sophisticated free energy calculations would be necessary to determine 
binding affinity or free energy of binding.

-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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