[Zinc-fans] basic question re: numbers

[Martin Stoermer]

Hi John,

Aha! this is the essential point I have been missing. Thanks for the  
clarification.

> * Compounds that were once available for purchase are no longer
> available as far as we know. These drop out of the ready-to-download
> subsets, but remain in ZINC, in case they reappear in a future catalog

Your point of purchasability is well made. It's vitally important, and  
to that end, when we embark on a VS screen one the first things we do  
is first constrain ourselves to the vendors who we know we can deal  
with in a timely manner. Sad to say there have been in the past  
several vendors who either didn't answer our calls, emails etc or  
wouldn't sell us anything less than a grands worth of stuff, or 1000  
compounds etc.

We are predominantly a synthetic chem lab, so we then look at any hits  
that come up that come from our non-core vendor list we look and see  
whether we would be better off making them (and analogues) ourselves  
in less time than it would take us to deal with an external supplier.  
Of course because we're an island in the Western Pacific, stuff takes  
a white to get here and we have to be realistic about what we order.

I personally am a big user of the "druglike" and "zinc_all" databases  
but not always in order to find things to buy. We do a lot of shape- 
matching work at the moment and I find that these sets with bigger  
sets of compounds that don't necessarily fit the "lead" concept often  
provide me with more inspiration for things (especially scaffolds)  
that I can go out and make in the lab (often one-offs to prove/ 
disprove a point).

I guess that we may not be your typical Zinc user, but there are many  
and varied things we can search for and find in Zinc and we're lucky  
to have you guys curating it for us.

thanks,
Martin

P.S.  No I'm not going to dish the dirt on vendors we're unhappy with...

>
> In our view the "lead like" (1M or so) and the "fragment like" (200K  
> or
> so) are the subsets that are most useful for ligand discovery and are
> probably all that most users will need or want. It is very important  
> to
> our own work to keep the purchsability rate of ZINC high - so we are
> rather cavalier about removing compounds from the exported subsets  
> that
> we do not think you will be able to acquire.
>
> I hope this is useful
>
> Good docking!
>
> John
> UCSF ZINC Team
>