[Zinc-fans] zinc compound ids

John J. Irwin jji at cgl.ucsf.edu
Tue May 30 13:47:54 PDT 2006

Hi Kaitlyn cc ZINC-fans

Sorry it is taking so long to fulfill your reasonable request. If you go to

zinc.docking.org (Note the 2006 release is now the default version of ZINC)
select "ZINC subsets" ->  http://blaster.docking.org/zinc/subset1/
select subset "10: everything" -> 
go to the bottom of the page, or click on "downloads"
To download a single representation of all 4.6M compounds (purchasable 
and non purchasable) click on "Single" in the "mol2" row on the right.
This is a csh script that will wget all the database slices.

The process of exporting these subsets is still in progress, but you can 
already get 50 slices today. More will become available tomorrow.

I hope this helps. I've been trying to create more useful and general 
structures of database subsets. This is an ongoing process. I welcome 
your feedback about how to make this more useful.

Best wishes,


Kaitlyn Hwang wrote:
> John,
> Is there a location where I can go to download all the mol2 mentioned in
> the properties.txt.gz?
> Thanks,
> Kaitlyn Hwang
> Argonne National Lab
> On Mon, 13 Mar 2006, John Irwin wrote:
>> Hi Kaitlyn Hwang
>> Sorry it's been so slow lately.
>> You can get properties for the Jan 05 ZINC release at
>> http://blaster.docking.org/zinc/properties.txt.gz
>> John
>>> -----Original Message-----
>>> From: zinc-fans-bounces at docking.org
>>> [mailto:zinc-fans-bounces at docking.org] On Behalf Of Kaitlyn Hwang
>>> Sent: Monday, March 13, 2006 12:31 PM
>>> To: zinc-fans at docking.org
>>> Subject: [Zinc-fans] zinc compound ids
>>> Hello,
>>> I want to get all the Zinc ids, and properites of the zinc
>>> from the database. Is there a fast way to request this
>>> besides using the browse/search tool? It takes a very long
>>> time to get the information and even longer waiting for the
>>> information to be downloaded.
>>> Kaitlyn Hwang
>>> Argonne National Lab
>>> _______________________________________________
>>> Zinc-fans mailing list
>>> Zinc-fans at docking.org
>>> http://blur.compbio.ucsf.edu/mailman/listinfo/zinc-fans

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