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

[Thomas Evangelidis]

I don't think AutoDock and Vina are suitable for peptide docking. I would
first try the FlexPepDocking module of Rosetta which does ab initio folding
of the peptide on the receptor, while moving the side-chains of the protein
but leaves its backbone intact. Rosetta implements a knowledge-based
scoring, which has been specifically designed for this task and is as fast
as Vina or AutoDock.

I would first do that and if I wouldn't get any reasonable results then I
would move to MD starting from the top scored protein-peptide complexes
created by Rosetta.

Thomas


On 4 October 2012 15:08, rama david <ramadavidgroup at gmail.com> wrote:

> 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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-- 

======================================================================

Thomas Evangelidis

PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
Panepistimioupoli-Zografou
157 71 Athens
GREECE

email: tevang at pharm.uoa.gr

          tevang3 at gmail.com


website: https://sites.google.com/site/thomasevangelidishomepage/