ZINC database

ZINC database

- ZINC20 : https://zinc20.docking.org/

- ZINC15 : https://zinc.docking.org/

- Papers

: ZINC: A Free Tool to Discover Chemistry for Biology (2005), https://doi.org/10.1021/ci3001277

: ZINC 15 – Ligand Discovery for Everyone (2015), https://doi.org/10.1021/acs.jcim.5b00559

: ZINC20—A Free Ultralarge-Scale Chemical Database for Ligand Discovery (2020), https://doi.org/10.1021/acs.jcim.0c00675

- Major classes

: https://zinc20.docking.org/majorclasses/epigenetic_regulator/predictions/

- PPT : The-ZINC-database-as-a-research-tool-to-simplify-docking-and-cheminformatics-workflows.pdf

 

 

http://ringo.ams.stonybrook.edu/index.php/ZINC15_Database

The ZINC15 database is an updated version of ZINC12 and contains over 100 million purchasable compounds for virtual screening.

What library do we prefer for virtual screens?
For zinc 15 it is recommended that we download small-molecule libraries across different vendors with user-specified properties (e.g. pH, formal charge, purchasability) using the "tranche browser" tool.
Now a library preferred by our group has the following properties.

Representation: 3D
Reactivity: Standard
Purchasability: In-stock (2 weeks)
pH: Ref (dominant form at pH 7.4)
Charge: -2, -1, 0, 1, 2
Preferred_subsets: drug-like (MW: 250~500, LogP: -1~5)

The total number of molecules in this library is 5385318 (as of 11/11/2016).

 

 

 

 

 

Reference

- https://bioinformaticsreview.com/20200720/how-to-download-small-molecules-for-virtual-screening-from-zinc-database/