ZINC − A Free Database of Commercially Available Compounds for Virtual Screening
Open accessAbstract
A critical barrier to entry into structure-based virtual screening is the lack of a suitable, easy to access database of purchasable compounds. We have therefore prepared a library of 727,842 molecules, each with 3D structure, using catalogs of compounds from vendors (the size of this library continues to grow). The molecules have been assigned biologically relevant protonation states and are annotated with properties such as molecular weight, calculated LogP, and number of rotatable bonds. Each molecule in the library contains vendor and purchasing information and is ready for docking using a number of popular docking programs. Within certain limits, the molecules are prepared in multiple protonation states and multiple tautomeric forms. In one format, multiple conformations are available for the molecules. This database is available for free download (http://zinc.docking.org) in several common file formats including SMILES, mol2, 3D SDF, and DOCK flexibase format. A Web-based query tool incorporating a molecular drawing interface enables the database to be searched and browsed and subsets to be created. Users can process their own molecules by uploading them to a server. Our hope is that this database will bring virtual screening libraries to a wide community of structural biologists and medicinal chemists.
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- Authors
- Irwin, J. J., & Shoichet, B. K.
- Affiliations
- University of California, San Francisco (US)
- Corresponding author
- Shoichet, Brian K.
- Venue
- Journal of Chemical Information and Modeling
- Publisher
- American Chemical Society (ACS)
- Published
- 2004-12-14
- Volume
- 45
- Issue
- 1
- Pages
- 177-182
- ISSN
- 1549-9596 (ISSN-L)
- 1549-960X
- PMC
- PMC1360656
- OpenAlex
- W2176516200
- Cited by
- 4,058
- References
- 31
- Citations by year
- 2026: 134 · 2025: 227 · 2024: 236 · 2023: 248 · 2022: 248 · 2021: 254 · 2020: 234 · 2019: 199 · 2018: 239 · 2017: 222 · 2016: 170 · 2015: 217 · 2014: 189 · 2013: 207 · 2012: 257
- FWCI
- 41.89
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Journal of Chemical Information and Modeling (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Institute of General Medical Sciences (GM71896, R01GM071896)
- Topics
- Physical Sciences › Computer Science › Computational Theory and Mathematics › Computational Drug Discovery Methods
- Physical Sciences › Chemistry › Organic Chemistry › Synthesis and Characterization of Heterocyclic Compounds
- Physical Sciences › Physics and Astronomy › Atomic and Molecular Physics, and Optics › Advanced Chemical Physics Studies
- Keywords
- ZINC database, structure-based virtual screening, chemical libraries, 3D molecular structure, protonation states, tautomerism, molecular docking, molecular properties
- MeSH terms
- Molecular Conformation, Drug Design, Molecular Structure, Databases, Factual, Libraries, Digital
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