[gmx-users] Interaction study for peptide-receptor..
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.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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