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
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
Justin,
Single mutation for four residue. The number of mutants is 4x19=76
Of course , that is a tiny peptide library.
Best
Shiyong
On Wed, Oct 10, 2012 at 9:06 AM, Justin Lemkul jalem...@vt.edu wrote:
On 10/9/12 8:43 PM, Liu Shiyong wrote:
Hi,
Your expectation from MD is too much
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
Hi,
Yes it is possible to screen peptides as ligand.
But for these following information is needed
1. Binding site of peptide and ligand
2. Which residues in peptide are important for binding.
After you simply do the mutation on the desired peptide.Performed the MD
upto 50 ns
Find the
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
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
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
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
On 10/4/12 8:08 AM, rama david 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
2012/10/4 rama david ramadavidgr...@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
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
On 10/4/12 8:40 AM, rama david wrote:
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
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
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
On 10/4/12 9:16 AM, rama david 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
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