[Zinc-fans] Dataset for retrospective study -reg

[Martin Stoermer]

Hi Mohamed,

if you want to use benchmarking sets, then I suggest you look at  
either DUD (http://dud.docking.org/ and http://pubs.acs.org/cgi-bin/ 
abstract.cgi/jmcmar/2006/49/i23/abs/jm0608356.html) or
the Astex/CCDC test sets (http://www.ccdc.cam.ac.uk/products/ 
life_sciences/gold/validation/)

Also, yes the MDDR  (MDL) and WDI (Derwent) are proprietary databases  
so they can't be uploaded to ZINC.  A small subset of FDA  approved  
drugs sourced from publicly accessible Tox data is available on Zinc.

cheers,
Martin
_____________________________________________________
   Dr. Martin Stoermer
   INSTITUTE FOR MOLECULAR BIOSCIENCE
   University of Queensland 4072 AUSTRALIA
   Phone: +61-7-3346 2988   Fax: +61-7-3346 2101
   Email:m.stoermer at imb.uq.edu.au
   http://www.imb.uq.edu.au
_____________________________________________________

On 25/10/2008, at 11:54 AM, Abdul Hameed, MohamedDiwanMo wrote:

> Dear Zinc users,
>
> I am in need of a dataset which can be used in retrospective  
> studies like comparison of virtual screening performance between  
> different methods. Most of the papers use commercially available  
> MDDR database or the world drug index. The reason being that known  
> drugs can be assumed as non inhibitor of the target being studied.  
> Is there any freely available dataset or any free for academic  
> dataset which can be used. I tried using FDA dataset in ZINC which  
> has around 2000 compounds. But there is big difference when  
> comparing performance using database of 2000 and 50,000 molecuels.
>
> One more question, can anyone tell me how these database are made?  
> Is the contents of MDDR or WDI are proprietary data? Can we make  
> such dataset on our own and make it available in Zinc.
>
> Your suggestion will be helpful.
>
> Thanks,
> Mohamed Diwan
> Graduate student
> College of Pharmacy
> University of Kentucky
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