Using ZINC to Acquire a Virtual Screening Library

John J. Irwin1

1 University of California San Francisco, San Francisco, California
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 14.6
DOI:  10.1002/0471250953.bi1406s22
Online Posting Date:  June, 2008
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The ZINC database of commercially available compounds contains biologically relevant representations of purchasable compounds in ready‐to‐screen formats. ZINC uses catalogs from over 50 compound vendors, changing from time to time to reflect newly available compounds and depleted stock. ZINC is available in subsets that reflect current opinion in the field such as “fragment‐like” and “lead‐like,” and has a facility to create additional small ad hoc subsets. ZINC has a search facility, as well as a service to process molecules that are not in ZINC by uploading them to a server. Curr. Protoc. Bioinform. 22:14.6.1–14.6.23. © 2008 by John Wiley & Sons, Inc.

Keywords: virtual screening; molecular docking; ligand discovery; small molecule libraries

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Table of Contents

  • Introduction
  • Basic Protocol 1: Download a Property‐Filtered Database Subset for Virtual Screening
  • Basic Protocol 2: Download a Vendor Database Subset for Virtual Screening
  • Basic Protocol 3: Searching ZINC
  • Basic Protocol 4: Create and Download a Custom Subset
  • Basic Protocol 5: Upload and Process Your Own Molecules
  • Commentary
  • Literature Cited
  • Figures
  • Tables
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Literature Cited

   Gasteiger, J., Rudolph, C., and Sadowski, J. 1990. Automatic generation of 3D‐atomic coordinates for organic molecules. Tetrahedron Comput. Methods 3:537‐547.
   Ihlenfeldt, W.D., Takahasi, Y., Abe, H., and Sasaki, S. 1992. In Daijuukagakutouronkai Dainijuukai Kouzoukasseisoukan Shinpojiumu Kouenyoushishuu (K. Machida and T. Nishioka, eds.) pp. 102‐105. Kyoto University Press, Kyoto, Japan.
   Keiser, M.J., Rother, B.L., Armbruster, B.N., Ernsberger, P., Irwin, J.J., and Shoichet, B.K. 2007. Relating protein pharmacology by ligand chemistry. Nat. Biotechnol. 25:197‐206.
Key References
   Huang, N., Shoichet, B.K., and Irwin, J.J. 2006. Benchmarking sets for molecular docking. J. Med. Chem. 49:6789‐6801.
  This paper describes the original public release of the ZINC database (version 4, released January 2005).
   Irwin, J.J. 2006. How good is your screening library? Curr. Opin. Chem. Biol. 10:352‐356.
   Irwin, J.J. and Shoichet, B.K. 2005. ZINC: A database of commercially available compounds for virtual screening. J. Chem. Inf. Model 45:177‐182.
Internet Resources
  The Zinc Web site. All the protocols described in this unit use the ZINC Web site exclusively.
  The Daylight Theory Manual describes SMARTS and SMILES.
  DOCK is an example of a docking program that can use molecules from ZINC.
  Commercially available chemical space, without the 3‐D representation.
  Source of pubchem molecules.
  Source of the OEChem chemical informatics toolkit, the Omega conformational sampling program, the Ogham depiction tools, the QuacPAC charge and electrostatics tools, and other tools used by ZINC. Also home of VIDA, a remarkable visualization tool, that works well with ZINC.
  Source of Cactvs, used to prepare ZINC and to support numerous key functions on the ZINC Web site.
  Source of mitools, used to calculate molecular properties for ZINC. Mitools are noteworthy for catching errors in SMILES that other packages miss.
  Source of ligprep, used to protonate and tautomerize molecules in ZINC.
  Source of AMSOL, the semiempirical quantum mechanics program by Cramer and Truhlar with a salvation‐adjusted Hamiltonian, used to calculate partial atomic charges and atomic desolvation penalties in ZINC.
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