ADL: docking libraries
forli at scripps.edu
Tue Nov 1 11:04:39 PDT 2011
have a look at 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
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
Please refer to Raccon user manual for further details:
Hope this helps,
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
> 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
> --- ADL: AutoDock List --- http://autodock.scripps.edu/mailing_list ---
Stefano Forli, PhD
Olson Molecular Graphics Laboratory
Dept. Molecular Biology, MB-112
The Scripps Research Institute
10550 North Torrey Pines Road
La Jolla, CA 92037-1000, USA.
tel: (858) 784-2055
fax: (858) 784-2860
email: forli at scripps.edu
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