Zusammen

The next stop on our tour of free chemistry databases and services on the Web is ZINC, a database of commercially-available compounds for virtual screening. Launched in 2004, ZINC has become a popular resource, both through its Web interface, and its inclusion in PubChem.

ZINC's main purpose is to provide pre-calculated values for molecular properties of common interest: 3D coordinates; molecular weight; polar surface area; desolvation; hydrogen bond donors/acceptors; rotatable bonds; logP; and charge. ZINC's molecules are compiled from the catalogs of large vendors, small vendors, and other sources including the ZINC user community. Structures can be located either by substructure or similarity, and/or by descriptor values. The entire ZINC database can be downloaded, although major portions can only be redistributed with written permission.

ZINC is one of the largest public-facing databases of small molecules, hosting nearly three million substances from 100 commercial suppliers.

One interesting feature of ZINC is its integration with the Similarity ensemble approach (SEA) service, a tool that relates proteins based on the set-wise chemical similarity among their ligands. For example, this ZINC record links to this SEA page.

ZINC offers a focused set of calculated properties for molecules provided by external depositors. As such, it may be useful to those doing docking experiments or building chemical databases.

Kudos

• Very large collection of curated content.
• Freely downloadable dataset.
• Friendly user community.

Ideas for Improvement

• Jmol applet failed to load on my Ubuntu/Firefox3 system, instead throwing AccessControlException (example) and hanging.
• Web page that shows status of file upload ("pending", "calculating", "done", "rejected", etc.). The current system of displaying a directory of files after upload is a bit confusing.
• New compounds feed (RSS/Atom).