On 2010-11-22 13.27, Thomas Evangelidis wrote:
With respect to protein folding, I want to fold a 42 amino acid loop
(part of a protein domain with known structure) which has no homologous
counterpart in PDB. Ab initio servers fail to assign a compact tertiary
structure to the loop, so I would like to see how MD tools can cope with
this problem. I 'm wondering if there is any way to keep the rest of the
protein rigid while running the simulation, cause the loop interacts
with the protein surface at many points.Is simulated annealing the right
approach? I'd appreciate any advice as I think the time scale of the
problem I described is accessible to MD.
I would go for REMD with position restraints on the C-alpha's of the
part of the protein for which you know the structure. To speed it up,
you might want to try loop prediction servers to get different starting
structures, however 42 is a long loop. Note that you will have to do
quite a long REMD > 100 ns I would think.
thanks in advance,
Thomas
On 22 November 2010 13:48, ms <deviceran...@gmail.com
<mailto:deviceran...@gmail.com>> wrote:
On 22/11/10 11:09, mohsen ramezanpour wrote:
Dear All
I am searching for a tutorial for learning how to do protein
folding with
Gromacs.
Do any one know such tutorials?
Please let me know them.
I don't think so because managing to fold a protein in a MD
simulation is no easy task. In theory, if you have a lot of patience
and a lot of computational resources, it's no different from a
normal MD simulation, but good luck even getting *close* to a folded
state.
So, it all depends on what you want really to know, and in this case
several techniques may help you (REMD, metadynamics, etc.) but I
think you have to read a lot of literature to make up your mind on
such stuff.
M.
Thanks in advance
Sincerely
Mohsen
--
Massimo Sandal, Ph.D.
http://devicerandom.org
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