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Three New Subsets - July 8, 2009

New ZINC subsets appeared today, Wed Jul 8, 2009:

#33 - goldilocks - not too this, not too that. just right. Try this set if you are getting too many "extreme" molecules that you do not like (although, getting extreme molecules may point to an underlying problem with your docking model)

#26 - all-now - chemical space in under two weeks.

#37 - sarah - back by popular demand. purchasable compounds under 250 Daltons. that's it. suitable for the model system sites

John

Updated/new ZINC subsets - Canada Day Edition

Happy Canada Day to everyone!

We have some new subsets that appeared on the ZINC website today (Jul 1, 2009).

1. "leads now", subset 21. 2.18M compounds (was 1.96M)
2. "drugs now", subset 23. 6.28M compounds (was 5.67M)
3. "clean CNS permeable", subset 39. This is a new subset, and has 344K cmpds.

As always, we welcome your feedback about ZINC. Please don't hold back. Your comments help us fix problems that we either have not noticed or have let slide.

For people having outstanding issues to which I have not yet responded:
a) thanks for your patience

Updated vendors

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.

-- John

New clean fragments subset released today

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.

Fragment-like now has 444K

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.

-- John

"all purchasable" is ready

The "all purchasable" subset of ZINC is ready for download. It contains over 13M compounds you can simply purchase, in ready-to-dock formats.

http://zinc.docking.org/subset1/6/index.html

-- John

DOCK Blaster news

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.

More soon.

John

A few subsets had duplicates - now fixed

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

Recent catalog updates

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.

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