Open Source for Virtual Screening

COMPUTATIONAL CHEMISTRY

Call it the Linux of molecular databases. Chemists have unveiled a new online collection of 2.7 million commercially available compounds, already prepared for use in docking programs--and it's free.

ZINC, which stands for ZINC Is Not Commercial, provides a much-needed resource for scientists in search of drug discovery leads, say its creators, associate professor Brian K. Shoichet and assistant adjunct professor John J. Irwin of the pharmaceutical chemistry department at the University of California, San Francisco [J. Chem. Inf. Model., 45, 177 (2005)].

Academic researchers have largely been limited to expensive commercial databases, such as the Available Chemicals Directory from Molecular Design Ltd. and ChemNavigator's database.

Free compound databases are beginning to crop up, however, such as Ligand.Info, ChemBank, and PubChem. But the compounds in many of these still aren't presented in a way that's easy to use in docking programs, and the databases require a lot of updating and maintenance, Shoichet says.

Funded by NIH, and with the agreement of chemical companies like Sigma-Aldrich and Pharmeks, ZINC can be used with numerous docking programs. Shoichet and Irwin have produced three-dimensional structures from two-dimensional information, weeded out insoluble forms, and calculated properties such as protonation states and number of rotatable bonds.

ZINC is generating positive responses from researchers like Heather A. Carlson, assistant medicinal chemistry professor at the University of Michigan, Ann Arbor. With its tools for mining data, ZINC makes screening more accessible, she says. "As far as free resources go, there's nothing like this."