ADL: Request for help protein protein docking

Sushil Mishra sushilbioinfo at gmail.com
Wed Feb 22 23:39:41 PST 2012


Dear Shahshank,

I think this is the place to discuss about AutoDock only. But, I would
like to add in the discussion that Kd or dG values from simple
empirical scoring functions used in Docking software should not very
much relied.  Free energy calculation is still one of the tricky job
for computational chemist. Primary objective of docking software are
to reproduce the binding mode of ligand correctly.

About Protein-Protein docking, I will suggest to read some of the
article by Prof Martin Zacharias.
(http://onlinelibrary.wiley.com/doi/10.1002/prot.20566/abstract)
He is working on a software named ATTRTACT. which could be helpful to you.


Good Luck!
Sincerely
Sushil


On Thu, Feb 23, 2012 at 8:18 AM, shashank rana
<shashank.bioinfo at gmail.com> wrote:
> Hi Dear friend,
>> I want joint 2 different proteins on their opposite terminal end(N and C).
>> Pls could you tell me some software which i use and if you know protocol
>> related to query pls send me.
>>
>    Pls sed me link of HADDOCK .
>
>>
>>
>> Regards,
>> Shashank
>>
>>
>>
>>
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