ZINC database

ZINC database
Content
Description	Chemical database
Data types; captured	Commercially available and annotated small molecules for virtual screening
Contact
Research center	University of California San Francisco
Laboratory	Irwin Lab ; Shoichet Lab
Authors	John Irwin, Brian Shoichet, and a cast of several
Primary citation	PMID 26479676
Release date	2004
Access
Website	ZINC
Miscellaneous
License	ZINC is free to use for everyone. Redistribution of significant subsets requires written permission from the authors.
Versioning	ZINC-22
Data release; frequency	continuously updated; static subsets regenerated quarterly or better.
Curation policy	continuously curated

The ZINC database (recursive acronym: ZINC is not commercial) is a curated collection of commercially available chemical compounds prepared especially for virtual screening. ZINC is used by investigators (generally people with training as biologists or chemists) in pharmaceutical companies, biotechnology companies, and research universities.^[1]^[2]^[3]

Scope and access

ZINC is different from other chemical databases because it aims to represent the biologically relevant, three dimensional form of the molecule.

Curation and updates

ZINC is updated regularly and may be downloaded and used free of charge. It is developed by John Irwin in the Shoichet Laboratory in the Department of Pharmaceutical Chemistry at the University of California, San Francisco.

Version

The latest release of the website interface is "ZINC-22". The database is continuously updated and as of 2023^[update] is claimed to contain over 37 billion commercially available molecules.^[4]

Uses

The database is typically used for molecule mining, a process in which Quantitative structure–activity relationships are used to find new compounds with improved biological activity, given a known starting point found, for example, by high-throughput screening.^[5]^[6]

References

^ Koes, D. R.; Camacho, C. J. (2012). "ZINCPharmer: Pharmacophore search of the ZINC database". Nucleic Acids Research. 40: W409 – W414. doi:10.1093/nar/gks378. PMID 22553363.
^ Doytchinova, Irini; Atanasova, Mariyana; Valkova, Iva; et al. (2018). "Novel hits for acetylcholinesterase inhibition derived by docking-based screening on ZINC database". Journal of Enzyme Inhibition and Medicinal Chemistry. 33 (1): 768–776. doi:10.1080/14756366.2018.1458031. PMC 6010092. PMID 29651876.
^ Olawale, Femi; Iwaloye, Opeyemi; Folorunso, Ibukun Mary; Shityakov, Sergey (2023). "In silico High-Throughput Screening of ZINC Database of Natural Compounds to Identify Novel Histone Deacetylase Inhibitors". Journal of Computational Biophysics and Chemistry. 22 (1): 11–30. Bibcode:2023JCBC...22...11O. doi:10.1142/S2737416522500466.
^ Tingle, Benjamin I.; Tang, Khanh G.; Castanon, Mar; Gutierrez, John J.; Khurelbaatar, Munkhzul; Dandarchuluun, Chinzorig; Moroz, Yurii S.; Irwin, John J. (2023). "ZINC-22─A Free Multi-Billion-Scale Database of Tangible Compounds for Ligand Discovery". Journal of Chemical Information and Modeling. 63 (4): 1166–1176. doi:10.1021/acs.jcim.2c01253. PMC 9976280. PMID 36790087.
^ Awale, Mahendra; Jin, Xian; Reymond, Jean-Louis (2015). "Stereoselective virtual screening of the ZINC database using atom pair 3D-fingerprints". Journal of Cheminformatics. 7. doi:10.1186/s13321-014-0051-5. PMC 4352573. PMID 25750664.
^ Panagiotopoulos, Athanasios A.; Konstantinou, Evangelia; Pirintsos, Stergios A.; et al. (2023). "Mining the ZINC database of natural products for specific, testosterone-like, OXER1 antagonists". Steroids. 199. doi:10.1016/j.steroids.2023.109309. PMID 37696380.

External links

ZINC database

[1] Koes, D. R.; Camacho, C. J. (2012). "ZINCPharmer: Pharmacophore search of the ZINC database". Nucleic Acids Research. 40: W409 – W414. doi:10.1093/nar/gks378. PMID 22553363.

[2] Doytchinova, Irini; Atanasova, Mariyana; Valkova, Iva; et al. (2018). "Novel hits for acetylcholinesterase inhibition derived by docking-based screening on ZINC database". Journal of Enzyme Inhibition and Medicinal Chemistry. 33 (1): 768–776. doi:10.1080/14756366.2018.1458031. PMC 6010092. PMID 29651876.

[3] Olawale, Femi; Iwaloye, Opeyemi; Folorunso, Ibukun Mary; Shityakov, Sergey (2023). "In silico High-Throughput Screening of ZINC Database of Natural Compounds to Identify Novel Histone Deacetylase Inhibitors". Journal of Computational Biophysics and Chemistry. 22 (1): 11–30. Bibcode:2023JCBC...22...11O. doi:10.1142/S2737416522500466.

[4] Tingle, Benjamin I.; Tang, Khanh G.; Castanon, Mar; Gutierrez, John J.; Khurelbaatar, Munkhzul; Dandarchuluun, Chinzorig; Moroz, Yurii S.; Irwin, John J. (2023). "ZINC-22─A Free Multi-Billion-Scale Database of Tangible Compounds for Ligand Discovery". Journal of Chemical Information and Modeling. 63 (4): 1166–1176. doi:10.1021/acs.jcim.2c01253. PMC 9976280. PMID 36790087.

[5] Awale, Mahendra; Jin, Xian; Reymond, Jean-Louis (2015). "Stereoselective virtual screening of the ZINC database using atom pair 3D-fingerprints". Journal of Cheminformatics. 7. doi:10.1186/s13321-014-0051-5. PMC 4352573. PMID 25750664.

[6] Panagiotopoulos, Athanasios A.; Konstantinou, Evangelia; Pirintsos, Stergios A.; et al. (2023). "Mining the ZINC database of natural products for specific, testosterone-like, OXER1 antagonists". Steroids. 199. doi:10.1016/j.steroids.2023.109309. PMID 37696380.

[1]

[2]

[3]

[4]

[5]

[6]