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

[Thomas Evangelidis]

I suppose by "full body dock" you mean rigid body docking, correct me if I
am wrong. In that case you could create initial starting structure for
flexible peptide docking. Rosetta accepts even coarse-grained models, namely
only the backbone, and then builds the full-atom structures.

Alternatively you could predict potential peptide binding sites on your
protein (i.e. by using this server http://pepsite.russelllab.org/index.html)
and the run SMD to force the peptide to attach to these putative binding
sites, and thus create initial coordinates for Rosetta. This approach is
more tedious. Nevertheless, flexible peptide docking with Rosetta takes
approximately 3 minutes per decoy on an average node and has sub-angstrom
accuracy. Posting a question in the Rosetta forum doesn't sound like a bad
idea.


On 12 April 2011 03:11, bharat gupta <bharat.85.monu at gmail.com> wrote:

> 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
>>
>>
>> website: https://sites.google.com/site/thomasevangelidishomepage/
>>
>>
>>
>>
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>
>
>
> --
> Bharat
> Ph.D. Candidate
> Room No. : 7202A, 2nd Floor
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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


website: https://sites.google.com/site/thomasevangelidishomepage/
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