[gmx-users] protein folding

[David van der Spoel]

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 <devicerandom at gmail.com
> <mailto:devicerandom at 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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-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se