ADL: ligand database

Mark Swingle mswingle at
Thu Apr 16 12:06:45 PDT 2009

On Thursday 16 April 2009 01:24:28 pm Wenjing.Shi at 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

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 ( ) 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 from 

Another possibility is to try DOVIS ( ) 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).



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