During May we have updated the following vendor catalogs in ZINC:
Aurora, BioBlocks, ChemDiv, ChemBridge, Enamine, Florida Heterocycles, IS-Pharm, KeyOrganics, Otava, Princeton, Shanghai Sinofluoro, TimTec, Vitas-M.
Hundreds of thousands of new compounds, and at least tens of thousands of depletions.
We have just exported fresh copies of all the "fragment" subsets. Coming up: "leads" subsets.
The "clean fragments" subset of ZINC, #12, was released today. It has 178K purchasable compounds, up from 126K in January 2009. "clean" ZINC subsets have stricter filtering rules applied to remove molecules that might not even be a problem. They are ideal for people who are willing to sacrifice a little chemical space coverage in return for a lower artifact rate.
A new version of the fragment-like subset was released today, Wednesday May 20 2009. It has 444K commercially available molecules, up from 319K in the previous version from January 2009.
The fragments-now subset (#22) has 423K, i.e. most fragments in ZINC are available from vendor stock and are not make to order.
"fragments" and "leads" are the two subsets of ZINC that we ourselves use most often.
The "all purchasable" subset of ZINC is ready for download. It contains over 13M compounds you can simply purchase, in ready-to-dock formats.
Dear DOCK Blaster users
Until I get it fixed, you are strongly urged to dock either "clean-leads" or "clean-fragments" (subsets 11 and 12 respectively).
For 95% of you, you probably want to only dock either subset 11 or 12.
If you downloaded any of the following subsets in the last two weeks, you may have downloaded two copies of each molecule due to a mistake that we fixed today.
The affected subsets are: bioblocks, chembridge BB, princeton BB, florida, otava, otava BB, otava on demand, timtec, ibs, asischem.
The dates are: around Apr 25 - May 6
The impact is: you might have two copies of each molecule.
The remedy is: download a fresh copy.
The worst that can happen is: you see the same molecule twice in your docking calculations.
The severity of this problem is: low
Over a dozen vendor catalogs have been recently updated in ZINC, maintaining our committment to deliver timely information. We update catalogs on a continuous basis, and we try to update every vendor catalog at least once a year, sometimes quarterly.
What does "updated" mean?
1. Compounds that are no longer in the vendor's catalog are marked "depleted"
2. All new eligible compounds are loaded in ZINC.
3. The vendor catalog is exported and publicly accessible in the "by vendor" pages.
Finally, the "everything" subset of ZINC is ready. As of May 7th at noon, it is complete.
Export started on April 21st, so even though ZINC is updated continuously, it is a pretty accurate reflection of the current contents. There are 21,603,031 molecules in the everything subset, which includes all public molecules in ZINC you can buy as well as ones you cannot (e.g. PubChem). Like all ZINC subsets, the "everything" subset is available for download in mol2 and SDF format. The "everything" subset is subset 10, and is available here: http://zinc.docking.org/subset1/10/index.html
In our ongoing attempt to raise the quality of molecules in ZINC we found 413,986 molecules that were broken in some way. Whereas this may sound like a lot, most of them will have been invisible to you. However, for complete transparency, we are making the file of all these deleted molecules available.
We strongly urge you NOT to use these molecules, because, as far as we can tell, there is something wrong with them.