[Zinc-fans] Donwload Zinc Database

[Andre Silva]

John,

Thank you for your fast reply.
I'll work here to download it.

Also, I'm planning to capture the results of a query in ZINC (that result 
page that comes up after you hit search)
My question is:
- There is an XSL schema defined for that or an interface to get query 
results ?

Thanks in advance,

Sincerely,

Andre L. Silva
andreramme at acm.org
PUC RS






"John J. Irwin" <jji at cgl.ucsf.edu> 
26/02/2009 14:42

To
Andre Silva <andre at starinfo.com.br>
cc
zinc-fans at docking.org
Subject
Re: [Zinc-fans] Donwload Zinc Database






I Andre

Thanks for your email and your question.

For instance, let's say you use the mol2 format of the "lead like"
subset, #1, for routine screening.  This is the one we ourselves use
most often.  Let's also say you want not only a single representation of
each molecule at pH 7, but other biologically relevant representations
near physiological pH (we call this the "usual" representations).

To get the script to download the database, there are four steps,
although the last one is optional.
1. rename your old version or delete it as appropriate
2. wget http://zinc.docking.org/subset1/1/usual.mol2.csh
3. csh usual.mol2.csh ; # this may need to run overnight, depending on
where you are

We also recommend you get a static copy of the purchasing information
that maps ZINC IDs to vendor catalog numbers:
4. wget http://zinc.docking.org/subset1/1/1_purch.xls
This means that if a compound becomes unavailable between the time you
download and the time you want to purchase it, you can still at least
find out where it used to be available from.  Some vendors are willing
to remake compounds, although the price to resynthesize will typically
be at least $750 rather than $25-100 for most in-stock compounds. (these
are just ball park figures)

There are other things you might get, and several variations on that
theme.  But this is what we figure is the most common scenario.  New
subsets are generated a couple of times a year.  We will start to
announce them via our RSS feed on docking.org, but we haven't been doing
that reliably up until now.

I hope this helps.

good docking

John


Andre Silva wrote:
>
> Hi Fans,
>
> I'm pretty new to this list and ZINC little I have a little experence
> using ZINC.
>
> My question is how is the procedure to download (and keep updated) a
> local replica of ZINC ?
>
> I could not find any document about this.
>
> Sincerely,
>
> Andre L. Silva
> andreramme at acm.org
> PUC RS
> ------------------------------------------------------------------------
>
> _______________________________________________
> Zinc-fans mailing list
> Zinc-fans at docking.org
> http://blur.compbio.ucsf.edu/mailman/listinfo/zinc-fans
> 

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