ADL: ligand database

Sargis Dallakyan sargis at
Thu Apr 16 11:40:56 PDT 2009

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?

Please read Using AutoDock 4 for Virtual Screening tutorial for 
instructions on how to do that:

> 2) If first question is possible, then how can I change SDF formate to PDB?

You can use openbabel to convert SDF formate to PDB:

You can also use PyRx [1] to convert SDB to PDBQT:

I recommends doing energy minimization before using 2D SDF files for 
virtual screening.



Sargis Dallakyan, Ph.D. - Research Programmer III
The Scripps Research Institute,
Dept. Molecular Biology,  MB-5,
10550  North Torrey Pines Road,
La Jolla,  CA 92037-1000
Tel: (858) 784-9559

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