ZINC Database

The ZINC Database of commercially available compounds for virtual screening is available for free from our website zinc.docking.org.

How to Cite ZINC

To cite ZINC, please reference Irwin and Shoichet, J. Chem. Inf. Model. 2005;45(1):177-82. This paper is also a good place to start to understand how ZINC has been assembled, and what it is good for. The rest of this document can be read as an update to that paper for things that have changed since going to press.

Filtering rules

To see the filtering rules in effect in ZINC, please see filtering.docking.org.

Molecules are not loaded if:

• They do not pass our generous filtering criteria.
• A failure occurs during processing.

Filtered compounds are now listed on the vendor page, with a justification.

Every compound in every supplier catalog has one of four fates:

• It has been loaded into ZINC
• It is depleted (not longer available) - and may still be in ZINC, marked depleted
• It was filtered out and never loaded. These are listed as "filtered out" on the vendor pages.
• It appeared in a newer catalog than has been loaded (version loaded is on vendors page)
• It failed at some stage of processing.

Which suppliers are included?

Please see the by-vendor page. If there is a catalog you would like to see loaded, please write to databases at docking.org.

Update frequency

New molecules are loaded into ZINC continuously. We foresee loading up to 10,000 new molecules every day, at least until 2012.

Old molecules are marked depleted in ZINC when they are removed from a supplier's catalog. For some suppliers, this is every day, for others, more like once a year. More than 50% of supplier catalogs are updated in ZINC at least twice a year.

Ready-to-download subsets are updated periodically. The last date of export is shown with the subset. If you find a too-old subset, tell us and we will update it.

Searching ZINC

The SMILES/SMARTS line below the JME applet in the ZINC Search page is interpreted as follows:

pattern - interpreted as SMARTS pattern N - molecules within Tanimoto N (0<N<100) of this SMILES. pattern N X Y - molecules within Tversky threshold N (0<N<100) having alpha=X/100, beta=Y/100. Thus:

c1ncccc1 100 0 100

matches molecules containing exactly pyridine, and

n1ccccc1 100 100 0

would match molecules that are a subgraph of pyridine.

The numbering is strange in the search results

We know about this. Sorry. We will fix it one day.

Problems with ZINC

We have collected all our problems on the problems page. If you have a problem with ZINC, please write support at docking.org.

How do subsets work?

We have pre-made a number of subsets (by vendor, by various criteria) that we hope you will find useful. When you search, you may download individual molecules or even all matching molecules in a variety of formats. However, you are limited to some number (typically around 1000, but it varies). The reason this is limited is that downloading large arbitrary collections of molecules puts a strain on our server. In order to download more, you may create a subset, by clicking on the "Create Subset" button in the "Search Results" browser. This will start an off-line subset preparation process, which will complete when resources allow (but allow at least 1 hr / 1000 molecules). It will appear in the "download subsets" (option #4) page.

Another way to create a subset, which isn't necessarily a strict subset, is to upload molecules to our server (option #5). These will again be processed in batch mode as resources permit. These subsets are not available on the browse subsets page, but instead via a URL that you will be given when you upload.

The goal of subsets is to facilitate research. You are encouraged to use these free tools. However, please note that these services are rather demanding on our server, and may be limited (or simply not function) from time to time. Thank you for your understanding.

Versions

• ZINC5 was released 1/1/2005 and is still available at blaster.docking.org/zinc5 ZINC5 was a major release, and completely superceded ZINC4, which is no longer available.
• ZINC6 was released 1/1/2006 and is still available at blaster.docking.org/zinc6. ZINC6 was a major release, in which all molecular geometries were re-created from SMILES.
• ZINC7 was released 1/1/2007 and is the current default version. It is an incremental release compared to ZINC6. Indeed, it looks very much like ZINC6.
• ZINC8 is will be released in June 2008 and will probably be a major release.

FAQ: ZINC numbers, mailing lists, uploading, XML RPC,