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

Justin Lemkul jalemkul at vt.edu
Thu Oct 4 14:45:33 CEST 2012

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


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