[gmx-users] protein folding

[mohsen ramezanpour]

I think you can produce a loop of 42 aminoacids by using PYMOL software,It
can produce a loop and it's result is a pdb file.
Besides,when you could produce your loop you can use it in your folding
process.because it is affected by other parts of protein as you said.
I think this can be a good approximation to what you want to do.
Best

On Mon, Nov 22, 2010 at 3:57 PM, Thomas Evangelidis <tevang3 at gmail.com>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.
>
> thanks in advance,
> Thomas
>
>
>
>
> On 22 November 2010 13:48, ms <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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>
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