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

[francesco oteri]

2012/10/4 rama david <ramadavidgroup at gmail.com>

> Hi francesco,
>
> Thank you For reply.
> I did docking but the result are not so impressive.
>

What does it mean "not so impressive"? I mean, do you have experimental
data
and the comparison with docking doesn't agree with experiments? Have you
generated
a sufficient number of complexes (say 100 or more)?

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??
>

It will change a lot the dynamics of your system and I don't think
calculations
will be more efficient!


> 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..
>

If you already have docking complexes, you can pick up one complex for each
peptide, to run an MD, or Free Energy  calculations.
It strongly depends by the experimentale data you have and what is the
target
of your work.


>
> 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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-- 
Cordiali saluti, Dr.Oteri Francesco