[gmx-users] Re : Simulation for prediction of binding between a peptide and protein

[bharat gupta]

but using docking I have to fix the grid and have to dock at that
position... which is not my objective ... I want the peptide to come and
bind own its own to the protein... I have heard of full body dock , in which
there is no need to define grid points , will that be useful ??


On Mon, Apr 11, 2011 at 2:02 PM, Thomas Evangelidis <tevang3 at gmail.com>wrote:

> You can try Rosetta for flexible peptide docking.
>
>
>
> On 11 April 2011 15:32, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
>
>> Hi,
>>>
>>> I want to know how can I predict where a designed peptide will bind to my
>>> protein target or not using simulation ... Can anybody guide me ??
>>>
>>
>> I don't think anybody has the computational resources to answer this
>> question with unguided MD. Docking programs are probably the way to get a
>> guide about what binding modes might be reasonable, but I don't know what
>> software might be fit for the purpose.
>>
>> Mark
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>
>
>
> --
>
> ======================================================================
>
> Thomas Evangelidis
>
> PhD student
>
> Biomedical Research Foundation, Academy of Athens
>
> 4 Soranou Ephessiou , 115 27 Athens, Greece
>
> email: tevang at bioacademy.gr
>
>           tevang3 at gmail.com
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-- 
Bharat
Ph.D. Candidate
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