[Zinc-fans] Donwload Zinc Database

[John J. Irwin]

Hi Andre

Andre Silva wrote:
>
> 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 ?
We do have an XML RPC interface to ZINC and other docking.org service. 
It can be found at http://xml.docking.org/.   Basic and incomplete
documentation is here
http://wiki.compbio.ucsf.edu/wiki/index.php/XML_RPC_Procedures
and
 http://wiki.compbio.ucsf.edu/wiki/index.php/XML_RPC_Services
Only a few of these services actually work reliably, but this should
give you an outline of where we plan to go.

If this is close to something you want or could use, write me off the
list telling me what services exactly it is that interest you, and we
will put some effort into making them work as you want.

John




>
> 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
> > ------------------------------------------------------------------------
> >
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> >  
>