ADL: ligand database

Mark Swingle mswingle at jaguar1.usouthal.edu
Thu Apr 16 12:06:45 PDT 2009


On Thursday 16 April 2009 01:24:28 pm Wenjing.Shi at lvh.com wrote:
> Hello,
>
> I'm a new user of Autodock. I need to find small molecules (from database
> of NCI) which can bind to the target MHC-peptid complexes. I downloaded
> this database with SDF formate, but had trouble in preapring them into
> ligand file. So my questions are:
> 1) Can I prepare batch of ligands and further do docking?
> 2) If first question is possible, then how can I change SDF formate to PDB?
>
> Thank you for your input!
>
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To get started, you might try this
 
http://autodock.scripps.edu/local_files/screening/NCI-Diversity-AutoDock-0.1.tar.gz

which has the NCI diversity set (~2000 compounds) in pdb and pdbq format 
(although I believe the ligand protonation states in many of the pdbq files 
are probably not correct). 

To make your own database, I would suggest getting ChemAxon's ( 
http://www.chemaxon.com/products.html ) java-based tools to process your sdf 
database and assign appropriate protonation states. Then convert the sdf 
database to separate mol2 files and process them with prepare_ligand4.py from 
ADT. 

Another possibility is to try DOVIS ( 
http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2542995 ) for 
virtual screening, which I believe can take an sdf file as input (I haven't 
used it yet, so I'm not certain of that).

Regards,

Mark





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