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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.

528 nitroguanines (NC(=N)N[N+](=O)[O-]) were repaired today

Dear ZINC Users

Today we repaired 528 nitroguanines that were incorrectly represented in ZINC. These changes are visible immediately in ZINC, and will be incorporated in new subsets as they are created going forward over the next month.

The problem was that some nitroguanines were cationic, some were anionic, and some were neutral.

692 isothiocyanates (R-N=C=S) were repaired today

Dear ZINC Users

We rebuilt 692 isothiocyanates that were broken today. These are available now in ZINC, and will be incorporated into static exported subsets going forward over the coming month.

The problem was that the isothiocyanates were often incorrectly protonated, thus R-[NH+]=C=S. The corrected form is neutral.

Please see our general notes on ZINC repair for terms and conditions and more background information: http://wiki.compbio.ucsf.edu/wiki/index.php/Notes_on_ZINC_repair

171 molecules removed from ZINC during cleanup today

We found 171 molecules that were mangled in ways that were not simple to fix. Thus we have deleted these molecules from ZINC. The source molecules will be reloaded with new ZINC IDs very soon. Some may already be loaded.

A good way to find molecules is to use the ZINC search feature, which has recently been improved, and which will continue to improve in the coming weeks and months.

A second good idea is to download purchasing information with each subset you download so that you have static information available in perpetuity.

ZINC Fragments subsets updated (again)

Dear ZINC Users

In the past week we have been housekeeping, resulting in better representations of the biologically relevant forms molecules and fewer errors. We have therefore released new versions of three ZINC fragment subsets as follows:

2 - "fragment like" - 374K (was 405K)
12 - "clean fragments" - 72K (was 81K)
22 - "frags now" - 335K (was 361 K)

(download here: http://zinc.docking.org/subset1/)

You will note a reduction of about 9%. These were incorrect duplicate representations of molecules. The new version is in our view much closer to correct.

New "fragment like" subsets available today

Dear ZINC Users

New versions of three ZINC subsets were released this morning:

2 - "fragment like" - 405K
12 - "clean fragments" - 81K
22 - "frags now" - 361 K

(download here: http://zinc.docking.org/subset1/)

A few points to note:

1. The number of fragments is about the same as it was, but don't be fooled: there has been tremendous turnover. At least 100,000 of these are new and about the same number are no longer available.

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