Dear ZINC Users

Thank you for your support of ZINC!

In the past 2 weeks we have had 5000 visits from 3000 unique visitors. Every weekday we receive about 450 visits from about 350 unique visitors. So far this month, you have downloaded over 2 TB of files from zinc.docking.org - our biggest month ever!

A big thank you to all our users. We are grateful for your support.

John Irwin
ZINC database

The ChEMBL12 annotations appeared in ZINC this morning.

http://zinc.docking.org/browse/targets/

The number of annotations increased as follows:

* Binding <= 10uM : 3490 (was 3333)
* Binding <= 1uM : 3032 (was 2969)
* Functional <= 10uM : 3032 (was 1998)
* ADME/T <= 10uM : 134 (was 128)

There were some mysterious absences in the previous version. Thus Muscarinic M1 Human (ACM1_HUMAN) was empty, and now has 820 purchasable. We don't know what that was due to, but it was obviously an error, and it is now fixed.

We released new shopping cart features yesterday. This includes

* rating molecules in your shopping cart (A+ to C-)
* new by-vendor purchasability reports
* a report that ranks molecules in the cart by your ranking

A video explaining these features is here:
http://www.youtube.com/watch?v=Pkfr-GdY5Ko

1. All of the special subsets http://zinc.docking.org/browse/subsets/special have been regenerated in the past week, fixing several minor problems. There is a video about this topic: http://www.youtube.com/watch?v=hteFp7g525U

2. Five by-property subsets have been regenerated in the past week:
clean-fragments, clean leads, frags-now, clean-shards and all-now
Half a dozen more subsets will be updated in the coming week.

We were reminded of an old problem with substructure searches and aromaticity models.

If you want to look for a fused ring system such as this: O=c2c1ccccc1c3ccccc23
some software considers the carbonyl C to be aromatic and some consider it to be aliphatic.
We are (still) working on making this consistent in ZINC. For now, if you do a substructure search, and if you have such a situation where an atom can be considered aromatic or non aromatic, we suggest the following workaround: use a wildcard "*", thus O=*2c1ccccc1c3ccccc23

Dear ZINC Downloaders

We have increased the size of mol2 database tranches for download. They now are 700 MB (CD-size) about 135 MB compressed. If this is too big for some of you, let us know. Each tranche contains about 128K molecules. The corresponding SDF files are about 550 MB (90 MB compressed). We will be transitioning to this file size from now through the end of the month as we rebuild all subsets.

Dear ZINC Users

We have standardized our protocol for creating subsets, and will update each subsets in the coming month to comply. All subsets created after Dec 14, 2011 comply. In many cases the changes were quite minor. There were no changes to the vendor and annotated catalogs. The download pages have been updated for clarity.

To summarize: Every molecule in every subset is purchasable with two exceptions:
* the "everything" subset (#10)
* annotated catalogs such as ChEMBL (purchasable bioactive compounds of each are available separately)

Dear ZINC Users

We have added scripts to our website to make it easier to download ZINC on Windows. We made a video about how to use the new scripts. http://www.youtube.com/watch?v=U0eG5SEVz8c

Good docking!

John

New ZINC database files in AutoDock "pdbqt" format are available at http://zinc.docking.org/pdbqt/. They have been tested with both AutoDock and the new AutoDock Vina. They are used in the Global Online Fight Against Malaria project and the FightAIDS@Home project on IBM's World Community Grid, but you can use them for any project you like.