Written and maintained by CASRAI Editorial Board
Last updated
The ZINC database is a free, publicly accessible database of commercially available (purchasable) small molecules, prepared in three-dimensional, ready-to-dock formats for virtual screening and ligand discovery. It is not about the element zinc: the name is a proper noun for a compound library that began in 2005 and has been republished in successive versions, most recently ZINC-22 (2023). This guide is for researchers who need to know what each version contains, how to find the right one and which paper to cite.
What the ZINC database is
ZINC was introduced by John J. Irwin and Brian K. Shoichet in 2005 as a free database of commercially available compounds for virtual screening. The original library held 727,842 molecules, each with 3D structure, protonation states, calculated properties (molecular weight, calculated logP, rotatable bonds) and vendor information, and it could be downloaded in formats ready for docking. Docking is the computational placement of a small molecule into a protein binding site to estimate how well it fits; ZINC exists so that the molecules being docked can actually be bought afterwards.
Versions and what each one covers
Size figures differ between versions because the database was rebuilt as the purchasable chemical space grew. Quote a number only together with the paper and year it comes from.
| Version | Year | What its own paper reports | Citation |
|---|---|---|---|
| ZINC | 2005 | 727,842 molecules with 3D structures, protonation states, properties and vendor information; free download in ready-to-dock form. | Irwin and Shoichet, PMID 15667143 |
| ZINC (screening library guide) | 2008 | Describes acquiring a virtual screening library from catalogs of more than 50 vendors, with subsets such as fragment-like and lead-like. | PMID 18551414 |
| ZINC | 2012 | Described as a free public resource for ligand discovery; searchable by structure, biological activity, physical property, vendor, catalog number, name and CAS number; custom subsets can be created, shared, docked and downloaded. | PMID 22587354 |
| ZINC 15 | 2015 | Over 120 million purchasable drug-like compounds, a quarter of them available for immediate delivery; links purchasable compounds to metabolites, drugs, natural products and annotated literature compounds; access by gene or target class. | PMID 26479676 |
| ZINC-22 | 2023 | Commercially accessible small molecules from multi-billion-scale make-on-demand libraries; new data organization for fast lookup of properties; analog searching through a graphical interface called CartBlanche. | PMID 36790087 |
Who runs it and what it covers
ZINC originates from the group of Irwin and Shoichet, and the papers above give the project address as docking.org (the 2012 paper gives zinc.docking.org; the 2023 paper gives cartblanche22.docking.org). The database does not hold experimental results of its own. It catalogs compounds that vendors sell, plus computed 3D conformations and properties. The ZINC-22 paper says the data are organized so that the molecular properties docking needs (conformations, partial atomic charges, calculated logP and solvation energies) can be looked up quickly, which had become slow with the older organization used in earlier versions.
What you can search
The papers describe these search and retrieval capabilities rather than a fixed interface, which has changed between versions:
- By structure and analogs. ZINC-22 supports analog searching with similarity methods that, according to the paper, scale sublinearly in the number of molecules.
- By identifiers and metadata. The 2012 version supported searching by vendor, catalog number, name and CAS number, as well as by biological activity and physical property.
- By target or class. ZINC 15 added access by gene or target class and connections to metabolites, drugs and natural products.
- By subset. Pre-defined subsets such as fragment-like and lead-like were described in 2008, and 2012 users could build and share custom subsets.
- By download route. The ZINC-22 paper states it is freely available through its web interface, via Globus and in the Amazon AWS and Oracle OCI clouds.
The address of the search page can change between releases; start from the address given in the most recent paper.
Citing ZINC
Cite the version you actually used, with its own paper, and record the date of access because the contents change. Cite ZINC-22 as Tingle BI, Tang KG, Castanon M, Gutierrez JJ, Khurelbaatar M, Dandarchuluun C, Moroz YS, Irwin JJ, J Chem Inf Model 2023, DOI 10.1021/acs.jcim.2c01253. For work done on earlier releases, cite the matching 2005, 2012 or 2015 paper in the table. A DOI is a persistent identifier for the paper, not the database snapshot; see DOI for how these identifiers work.
Strengths and limits
- Free and openly described. Each version is documented in a peer-reviewed paper, and the ZINC-22 record in Europe PMC carries a CC BY license.
- Purchasable by design. Its focus on commercially available compounds means hits can be ordered for testing, as the 2005 and 2015 papers emphasize.
- Not a bibliographic database. It lists compounds and calculated properties; it is a different kind of resource from literature indexes such as MEDLINE or from interaction resources such as the STRING database.
- Numbers are version-specific. Compound counts range from 727,842 in 2005 to multi-billion-scale make-on-demand libraries in 2023, so a figure without a year is not citable.
- Computed properties. Conformations, charges and logP values are calculated, not measured.
FAQ
Is the ZINC database about the element zinc?
No. ZINC is the name of a compound library for virtual screening. Searching for the element or for zinc supplements will not lead to it; look for docking.org or the papers cited above.
Is the ZINC database free?
The papers describe it as a free resource: the 2005 paper offers free download, the 2012 paper calls it a free public resource and the 2023 paper states ZINC is freely available to everyone.
Which ZINC version should I cite?
The one whose data you used. ZINC-22 (2023) is the most recent paper listed here; ZINC 15 (2015) and the 2012 and 2005 papers document earlier builds.
What is ZINC used for?
Preparing libraries of purchasable molecules for molecular docking and other ligand-discovery work, and finding analogs of a compound that can be bought.
Sources
- Irwin JJ, Shoichet BK. ZINC: a free database of commercially available compounds for virtual screening. 2005. PMID 15667143. Europe PMC, read 2026-11-08.
- Using ZINC to acquire a virtual screening library. 2008. PMID 18551414. Europe PMC, read 2026-11-08.
- ZINC: a free tool to discover chemistry for biology. 2012. PMID 22587354. Europe PMC, read 2026-11-08.
- ZINC 15: Ligand Discovery for Everyone. 2015. PMID 26479676. Europe PMC, read 2026-11-08.
- Tingle BI et al. ZINC-22: A Free Multi-Billion-Scale Database of Tangible Compounds for Ligand Discovery. J Chem Inf Model 2023. PMID 36790087, DOI 10.1021/acs.jcim.2c01253. Europe PMC, read 2026-11-08.
