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

[Thomas Evangelidis]

CABS is able to conduct blind docking of peptides. You may also use the
predicted poses as starting structures for the Rosetta. Have a look at this:

http://www.springerlink.com/content/p6223376886054m6/



On 12 April 2011 10:22, Thomas Evangelidis <tevang3 at gmail.com> wrote:

> 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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>>>
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>>
>>
>>
>> --
>> Bharat
>> Ph.D. Candidate
>> Room No. : 7202A, 2nd Floor
>> Biomolecular Engineering Laboratory
>> Division of Chemical Engineering and Polymer Science
>> Pusan National University
>> Busan -609735
>> South Korea
>> Lab phone no. - +82-51-510-3680, +82-51-583-8343
>> Mobile no. - 010-5818-3680
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>>
>>
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>>
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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/
>
>
>
>


-- 

======================================================================

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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