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

rama david ramadavidgroup at gmail.com
Thu Oct 4 14:08:05 CEST 2012


Hi francesco,

Thank you For reply.
I did docking but the result are not so impressive.
I used vina and autodock.
I also did virtual screening in autodock but the result are not upto the
mark.

Is the freezing of group can affect my system?? How much efficiency I get
by these work??
As these group are going to freeze in four simulation so if it affect one
ligand it  affect other
ligand also.

I read article that did the work like me ,
they sliced the binding residues and  used the inert solid sphere to
support binding residues
instead of the freezing group other group.

I think both way should have same effect..Am I right or wrong??

If you have any other way please suggest it..

With best wishes and regards
Rama david


On Thu, Oct 4, 2012 at 5:07 PM, francesco oteri
<francesco.oteri at gmail.com>wrote:

> Hi,
> as far as I know, freezing just set velocities to 0 so you gain nothing
> freezing atoms.
>
> By the way, have you tried docking? It takes into account multiple
> conformation and
> orientation of the peptide and, depending upon the implemented algorithm,
> also
> protein sidechain orientation.
>
> Francesco
>
>
> 2012/10/4 rama david <ramadavidgroup at gmail.com>
>
> > thank you Justin for reply.
> >
> > I dont know about long range interactions.
> > But as I freeze the group I think it will improve my computational speed.
> > So is there any way to find out or decide which group should be
> > freeze, and which group should affect my interaction most probably??
> >
> > Should I do Essential Dynamics ??? or Principle component analysis ???
> >
> > Would you suggest me any general protocol for such work??
> >
> > Thank you in Advance
> >
> >
> > With Best Wishes and regards.
> > Rama David
> >
> > On Thu, Oct 4, 2012 at 3:57 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> >
> > >
> > >
> > > 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
> > >
> > > --
> > > ==============================**==========
> > >
> > > 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<
> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> > >
> > > ==============================**==========
> > > --
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> --
> Cordiali saluti, Dr.Oteri Francesco
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