[gmx-users] Interaction study for peptide-receptor..
rama david
ramadavidgroup at gmail.com
Thu Oct 4 14:40:36 CEST 2012
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.
That will tell me about binding affinity ( Hope so )
These is my basic idea.
Is any other way to do the same thing..
With best wishes and regards
Rama David
On Thu, Oct 4, 2012 at 5:47 PM, francesco oteri
<francesco.oteri at gmail.com>wrote:
> 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
> --
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