[Zinc-fans] unable to retreive zinc structure from database

Brian Moldover moldoverb at gmail.com
Wed Feb 16 16:12:08 PST 2011

Hi John,

I wasn't looking at purchasing information, I was simply trying to look up
that ZINC ID online. I grep'd through the flat files (all the sds files for
subset #3) I downloaded onto my server and it was found. When I query by
Zinc ID on the search page, it is not found. That's the example I gave. 

Not knowing how they are indexed in the database for searching, I'd guess
either the index is corrupt or somehow there are data missing. Or am I
misunderstanding how the flat files for download and online searchable
database are related? 

Purchasing is an entirely different nightmare. Some of these vendors are
interesting, to say the least. 



-----Original Message-----
From: John Irwin [mailto:jir322 at gmail.com] 
Sent: Tuesday, February 15, 2011 12:35 PM
To: Brian Moldover
Cc: zinc-fans at mailman.docking.org
Subject: Re: [Zinc-fans] unable to retreive zinc structure from database

Hi Brian

There is TREMENDOUS turnover in the chemical marketplace, and we can hardly
keep up.  Every year, over a million compounds become available and over a
million disappear.

It is very important for us to provide libraries of purchasable compounds,
and as a consequence, we update ZINC continuously. A new export of subset 3
was started a few days ago, but it takes more than a week to generate, since
the mol2 files alone are 50GB gzipped.

So, we regret you've had this bad luck with purchasing.

In the future, you are encouraged to download the Purchasing Information
associated with the subset you download. This is a static file containing
complete purchasing info for every molecule in tab delimited format.

Please note that this is not necessarily a solution to your problem.
Just because you know that company X used to sell that compound may still
not help you.  Policies vary, but it will often be expensive to source a
compound whose stock is depleted.

Since you mentioned ZINC50380596, I just downloaded the purchasing info for
subset 3 which is still on the ZINC website. I did

grep ZINC50380596   3_purch.xls

I got

  Enamine-REAL    Z960720376

Thus you could try to contact them, but their current catalog says they do
not sell it anymore.  Note that this is a "make on demand"
catalog, and so I searched the current "on the shelf" Enamine catalog, which
you can find on our website.  Unfortunately, this compound does not appear
to be in there either.

Good docking!


On Wed, Feb 16, 2011 at 6:14 AM, Brian Moldover <moldoverb at gmail.com> wrote:
> Hi all,
> I have downloaded the Zinc subset #3, drug-like, for screening and 
> similarity searching. I tried using some of the ID's to search ZINC 
> online, and they are not found. Of the 13 ID's I looked at, only one was
> I've tried using both ZINC ID and converting them to a SMILES string 
> for searching, and they are still not found.
> An example is ZINC50380596, which is in file vi 3_p0.119.sdf in the 
> above subset.
> Any ideas?
> -Brian
> _______________________________________________
> Zinc-fans mailing list
> Zinc-fans at mailman.docking.org
> http://mailman.docking.org/mailman/listinfo/zinc-fans

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