ADL: docking libraries

Stefano Forli forli at scripps.edu
Tue Nov 1 11:04:39 PDT 2011


Hi Mohsen,

have a look at Raccoon:

  http://autodock.scripps.edu/resources/raccoon

it should be the tool you are looking for.

If you align your structures so that all the active sites are overlapped and can be 
covered in a single grid box (then, a single GPF template file), you can use the Multiple 
Conformations mode.

To align receptor structures there are many tools you can use, but for 50 files I would go 
for something that can be used from the command line (i.e. LovoAlign 
http://www.ime.unicamp.br/~martinez/lovoalign/home.html )

Please refer to Raccon user manual for further details:

http://mgldev.scripps.edu/raccoon/Raccoon_v1.0_user_manual.pdf

Hope this helps,

Stefano


On 11/01/2011 02:53 AM, mohsen ramezanpour wrote:
> Dear users
>
> I have 2 libraries of ligands and proteins(50 ligands and 50 proteins)
> and I am interested to dock all ligands to all proteins.
>
> It seems to me that I have 2 solutions for this problem:
> 1- I have to *dock each ligand to all proteins* and repeat this process for
> *all ligands*
> 2-I have to *dock each protein to all ligands* and repeat this process for *all
> proteins*
>
> Which one is possible and easier with Autogrid and Autodock?
> Note: each protein have only one Active site,So all ligands will dock to
> the same Active site
>
> Please let me know how can I solve this problem
> Do you know any tutorial related to this problem?
>
> Thanks in advance for your ideas
> Best
> Mohsen
> ________________________________________________
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-- 
  Stefano Forli, PhD

  Research Associate
  Olson Molecular Graphics Laboratory
  Dept. Molecular Biology,  MB-112
  The Scripps Research Institute
  10550  North Torrey Pines Road
  La Jolla,  CA 92037-1000,  USA.

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     email: forli at scripps.edu
     http://www.scripps.edu/~forli/


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