ZINC – a tool that simplifies the process of discovering small molecules for biological targets

Wednesday, September 21, 2011 - 16:30
TH 331
John J. Irwin, Ph.D. (UCSF - Pharmaceutical Chemistry)

ZINC (ZINC Is Not Commercial) is a free public resource for the discovery, prioritization and acquisition of chemical reagents for biology. The database contains over 13 million commercially available “drug like” molecules in biologically relevant representations that may be downloaded in popular, ready-to-dock formats. The website enables searches by structure, biological target, physical property, vendor and catalog number and combinations of these. Small custom subsets may easily be created, saved, edited, shared, downloaded or sent directly to a vendor for purchase via a shopping cart mechanism.

ZINC was originally designed for molecular docking (see Figure), a widely-used and pragmatic way to discover new small molecules that bind to proteins, and thus may be useful for pharmaceutical and biological research.

The new interface to ZINC was designed and written by an SFSU student, Teague Sterling, who now works full time at UCSF.


John Irwin is Adjunct Associate Professor of Pharmaceutical Chemistry at the University of California San Francisco. For the past decade he has been working on computational ligand discovery, first at Northwestern University Medical School and since 2003 at UCSF. He creates and curates software tools and databases for ligand discovery including:

* ZINC, a free database of commercially available compounds for virtual screening

* DOCK Blaster, a free target based virtual screening web service

* DUD, a dataset for benchmarking target-based virtual screening methods and

* SEA, the Similarity Ensemble Approach for predicting biological targets for molecules.