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three ring systems cleaned up

Dear ZINC Users

Today we repaired molecules matching three SMARTS patterns in ZINC that had issues, as follows:

1. 6511 cases of imidazo[1,2-a]pyridine-2-ester or -2-amide, having the SMARTS pattern: [O,N]C(=O)c2cn1ccccc1n2. For instance, the ester (these are ZINC IDs) 05983327, 05983011, 07240926 or the amide 12630083. We deleted the wrongly protonated rings.

2. 24,110 cases of imidazo[2,1-b]thiazole, having the SMARTS pattern c2cn1ccsc1n2. For instance, 08281641, 04864557, 12531418. We deleted the wrongly protonated rings.

chEMBL08 is out

ChEMBL08 was released over the weekend. Better act quickly before it is obsoleted by ChEMBL09.

Updating refererence SMILES of molecules in ZINC

Dear ZINC Users

We updated the canonical SMILES of molecules in ZINC today. The 3D representations of the molecules are unchanged.

As you know, SMILES can often be written in multiple ways. Today we applied a new canonicalization scheme. You should notice absolutely nothing, except that the 2D representations of molecules should be better in a few cases.

All together, approximately 1M of the 18 M molecules in ZINC were affected.

-- John

Fixed 122,208 of [ND1]c1cc(=O)[nH]cn1 containing molecules

Dear ZINC Users

We found a problem with molecules containing [ND1]c1cc(=O)[nH]cn1.
These molecules are now correct in the database.
We are re-creating subsets now.

-- John

322K benzimidazoles fixed today

We deleted some incorrect representation of benzimidazoles today. This change is effective immediately in ZINC, but the exported subsets will be re-created as fast as possible. Generally, lead like and fragment like will be ready within a week, while drug like takes a little longer.

Here are the details:

Anilinic mea culpa

Dear ZINC Users

We have deleted some molecules from ZINC. These molecules were wrong (broken), and will be reloaded with new ZINC IDs in the coming weeks. We try to always advertise molecules we delete permanently here: http://zinc.docking.org/broken/

OK, here are the details:

Today we found 19,623 molecules in which a secondary aniline was protonated, thus matching the SMARTS: a1aaaac1[ND2H2]

Updated ZINC drug-like subsets

Dear ZINC Users

Today we are releasing updated versions of some popular ZINC subsets. These are:

3. "drug-like" 12.1M molecules
13. "clean-drug-like", 3.7M molecules
23. "drugs-now", 5.7M molecules

The clean ZINC subsets have stricter filtering rules applied. For more info see http://filtering.docking.org/. For the record, we ourselves often use the less highly filtered subsets. The best choice will depend on the project. Use your judgement.

We are also releasing the "all purchasable" subset and the "everything" subset.

6. "all purchasable", 16.7M molecules

New instant similarity in ZINC

Dear ZINC Users

We pre-compute and maintain links between the most similar molecules in ZINC. This gives you instant access to analogs without requiring a search be performed. A new interface will appear shortly to give access to this instant similarity.

We are loading the similarity table now. It is slow going, because each ZINC molecule must be compared against every other ZINC molecule. It will take about a month.

Of course, you can still search for analogs the not-so-slow way using ZINC Search.

New ZINC Lead-Like subsets now available

Dear ZINC Users

Today we are releasing new lead-like subsets of the ZINC database. These are by far our most popular subsets, as they attempt to capture the current thinking of the field for what constitutes a good virtual screening library. Download page is here: http://zinc.docking.org/subset1/

The statistics are:

Set 1: "lead like" 3.7 M
Set 11: "clean leads" 727K
Set 21: "leads now" 1.8M

To recap:

* "leads now" are for immediate delivery. Subset 1 includes "make on demand" which typically take 6-8 weeks for delivery due to synthesis.

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