On 10/9/12 9:17 PM, Liu Shiyong wrote:
Justin,
Single mutation for four residue. The number of mutants is 4x19=76
Of course , that is a tiny peptide library.
Of course one can design many different mutants with a 4-residue peptide (far
more than 76 in fact, considering all possible combinations of all 20 amino
acids), but I do not believe that is the intent of the OP here. Referring to
the original post:
http://lists.gromacs.org/pipermail/gmx-users/2012-October/075182.html
It seems that 4 total simulations are intended (perhaps 4 simulations with
replicates).
-Justin
On Wed, Oct 10, 2012 at 9:06 AM, Justin Lemkul <[email protected]> wrote:
On 10/9/12 8:43 PM, Liu Shiyong wrote:
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.
I would hardly call 4 different mutants a library. Plenty of methods exist
to enhance the sampling of such systems and have been used to great effect.
Computationally expensive to pull off properly? Yes. Impossible? In this
case, I would say no.
-Justin
On Thu, Oct 4, 2012 at 9:16 PM, rama david <[email protected]>
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
<[email protected]>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 <[email protected]> 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
<[email protected]>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 <[email protected]>
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 <[email protected]>
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
--
==============================**==========
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Thomas Evangelidis
PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
Panepistimioupoli-Zografou
157 71 Athens
GREECE
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[email protected]
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========================================
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Research Scientist
Department of Biochemistry
Virginia Tech
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http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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