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

Wed Oct 10 02:43:26 CEST 2012

Hi,

Your expectation from MD is too much than reality.

Peptide design is an open problem. Lots of elegant protocols are
available. However, to my understanding, the core problem is still
about protein-peptide docking and scoring. MD simulation only helps on
some special cases. It is impossible that MD simulation is used to for
screening peptide library.

Best

Shiyong

On Thu, Oct 4, 2012 at 9:16 PM, rama david <ramadavidgroup at gmail.com> wrote:
> Thank you  for reply,
>  I read the recently published article in Biochemistry.
> They worked on the same receptor that I am working.
> ( as I mention in my previous mail)
> They used NAMD software and I am using gromacs.
> They sliced the  receptor binding site and used the the solid support
> to the binding site and did simulation.
>                So if I freeze  the group is it will ok ??
> Is it possible in gromacs to fix the residue on solid immobilized surface.
> If it is how to do it??
>
> my question is How to decide which group are remove and which group should
> keep in simulation.????
>
> thank you in advance
> Thank you for giving your valuable time and advice to me.
>
> With best wishes and regards,
> Rama david
>
>
>
>
>
>
> On Thu, Oct 4, 2012 at 6:11 PM, Thomas Evangelidis <tevang3 at gmail.com>wrote:
>
>> 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/
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-- 
Shiyong Liu
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Biomolecular Physics and Modeling Group, Department of Physics,
Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
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刘士勇
华中科技大学物理学院  生物物理模建小组
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