[Zinc-fans] Problem with Search and Browse

[Tarun Jain]

Dear John,

Thank you very much for the useful information. I can understand the
vast chemical space ZINC Team is handling. All the very best for your
efforts.

Regards,
Tarun

-----Original Message-----
From: John J. Irwin [mailto:jji at cgl.ucsf.edu] 
Sent: Thursday, January 15, 2009 11:06 AM
To: Tarun Jain
Cc: zinc-fans at docking.org
Subject: Re: [Zinc-fans] Problem with Search and Browse

Hi Tarun

Tarun Jain wrote:
>
> Dear Zinc-Fans,
>
>  
>
> On the ZINC database, under the Search and Browse, I am trying to
> search for an entry '*ZINC08368114*'. I am repeatedly getting this
> message:
>
> *No hits found select s.sub_id,s.smiles from substance s, protomer p,
> catalog_item ci, catalog c where s.sub_id = ci.sub_id_fk and
> ci.cat_id_fk = c.cat_id and c.free=1 and p.sub_id_fk = s.sub_id and (
> s.sub_id = 8368114 ) limit 0,500*
>
Try ZINC7 : http://zinc7.docking.org/srchdbk.pl?zinc=8368114

The reason you can't find that molecule in ZINC 8 is that - as far as I
can tell - it is no longer for sale.  We eliminate molecules from ZINC
as soon as we know they are no longer for sale, because most people do
not like ordering compounds they can't get, and vendors don't like
having to say they no longer have it.

All that said, Enamine-REAL is one of two databases where we are still
loading the latest data. Why? There are over 10M compounds (achiral) in
this catalog.  We'll still be loading in 2010!  since we  load fewer
than 1M new compounds per month. You can get a copy of everything we
received from the vendor and search for yourself here:
http://zinc.docking.org/catalog/enamine-v.in
(accessible  from ZINC -> Synthesis-on-demand->Enamine-REAL -> catalog
information)

> **
>
> Also, when I am uploading a list of zinc codes as a text file (50 -
> 100 codes), I don't retrieve the information of all the codes.
>
> Please suggest if it is a temporary problem or I have to modify my
> search. I have seen a similar problem reported by Marc.
>
Again, we eiminate molecules that can no longer be purchased as soon as
we are told by the vendor.  Sometimes that happens every day.  We
recommend trying to search in ZINC 7, but caution that although you may
find the molecule in ZINC 7, that does not mean you can buy it.

Finally, we suggest to everyone to download the "purchasing info" when
downloading ZINC subsets.  This gives you the original catalog supplier
info for each ZINC ID in perpetuity, so you do not need to come back to
ZINC to figure out how to buy a compound.   But caution: there is rapid
turnover of compounds in the market place.  We see that over 1M
purchasable compounds become depleted (unavailable) every year, and
another new 1M++ come onto the market. Rapid turnover indeed!  Welcome
to my life.  We try to update ZINC regularly, on a rolling basis. I hope
you find this helpful and not too disappointing.

Good docking!

John
UCSF ZINC Team
>
>  
>
>  
>
> Thanks & Regards,
>
> Tarun Jain, Ph.D.
> Research Scientist, Molecular Modeling, 
> Department of Medicinal Chemistry, R&D III
> Ranbaxy Research Laboratories
> PlotNo. 20, Sector - 18
> Gurgaon - 122001, Haryana
> India
> Ph.- 91-124-2342001-10 Ext. - 5210
>
>  
>
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