ZINC: A Free Tool to Discover Chemistry for Biology

ZINC: A Free Tool to Discover Chemistry for Biology

May 15, 2012 | John J. Irwin, Teague Sterling, Michael M. Mysinger, Erin S. Bolstad, and Ryan G. Coleman
ZINC is a free public resource for ligand discovery, containing over 20 million commercially available molecules in biologically relevant representations. The database allows users to search by structure, biological activity, physical property, vendor, catalog number, name, and CAS number. Users can create, edit, share, dock, and download subsets of molecules, and convey them to vendors for purchase. The database is curated for high purchasing success and is freely available at zinc.docking.org. ZINC is a research tool for investigators seeking chemical matter for their biological targets. It incorporates purchasable compounds from over 100 vendors and annotated compounds from over 20 databases. Since its first appearance eight years ago, ZINC has grown over 10-fold in size, with improved 3D molecular representations and new features. ZINC now supports other chemoinformatic techniques. A useful ligand discovery database should be large, contain purchasable compounds, be relevant, and be in biologically applicable forms. It should be available in useful subsets, easy to search and download, and ready to use without additional processing. The database should include as many catalogs of biologically relevant molecules as possible. Hypothesis testing of computationally predicted ligands is fastest if the compounds are purchasable. ZINC has a unique focus on biologically relevant molecular representations for docking, but overlaps with other databases. It includes purchasable molecules from over 134 commercial supplier catalogs and 36 annotated catalogs. Molecules are prepared in multiple biologically relevant 3D forms, organized into four pH ranges. The database allows users to search by molecular similarity, substructure, physical properties, delivery time, and name and CAS number. ZINC has been improved with new features, including new catalog types, improved functional group filtering, and improved biologically relevant 3D molecular models. It now includes purchasable bioactive compounds (PBCs) and offers a variety of search options, including by target, delivery time, and physical properties. The user interface has been redesigned to allow for new queries and to facilitate research. ZINC now allows users to create and manage shopping carts, prioritize compounds, and generate decoys for docking benchmarks. It also provides a variety of report formats and supports scriptable interfaces for advanced users. ZINC aims to follow the 90/90 rule: 90% of the molecules in ZINC are verified as being for sale within 90 days. ZINC can be used to discover chemical reagents for biology, including acquiring general screening libraries, target-focused libraries, and libraries of bioactive compounds. It can also be used to identify specialist vendors and prioritize hits for purchase. ZINC is a valuable resource for researchers in the field of chemical biology and medicinal chemistry.ZINC is a free public resource for ligand discovery, containing over 20 million commercially available molecules in biologically relevant representations. The database allows users to search by structure, biological activity, physical property, vendor, catalog number, name, and CAS number. Users can create, edit, share, dock, and download subsets of molecules, and convey them to vendors for purchase. The database is curated for high purchasing success and is freely available at zinc.docking.org. ZINC is a research tool for investigators seeking chemical matter for their biological targets. It incorporates purchasable compounds from over 100 vendors and annotated compounds from over 20 databases. Since its first appearance eight years ago, ZINC has grown over 10-fold in size, with improved 3D molecular representations and new features. ZINC now supports other chemoinformatic techniques. A useful ligand discovery database should be large, contain purchasable compounds, be relevant, and be in biologically applicable forms. It should be available in useful subsets, easy to search and download, and ready to use without additional processing. The database should include as many catalogs of biologically relevant molecules as possible. Hypothesis testing of computationally predicted ligands is fastest if the compounds are purchasable. ZINC has a unique focus on biologically relevant molecular representations for docking, but overlaps with other databases. It includes purchasable molecules from over 134 commercial supplier catalogs and 36 annotated catalogs. Molecules are prepared in multiple biologically relevant 3D forms, organized into four pH ranges. The database allows users to search by molecular similarity, substructure, physical properties, delivery time, and name and CAS number. ZINC has been improved with new features, including new catalog types, improved functional group filtering, and improved biologically relevant 3D molecular models. It now includes purchasable bioactive compounds (PBCs) and offers a variety of search options, including by target, delivery time, and physical properties. The user interface has been redesigned to allow for new queries and to facilitate research. ZINC now allows users to create and manage shopping carts, prioritize compounds, and generate decoys for docking benchmarks. It also provides a variety of report formats and supports scriptable interfaces for advanced users. ZINC aims to follow the 90/90 rule: 90% of the molecules in ZINC are verified as being for sale within 90 days. ZINC can be used to discover chemical reagents for biology, including acquiring general screening libraries, target-focused libraries, and libraries of bioactive compounds. It can also be used to identify specialist vendors and prioritize hits for purchase. ZINC is a valuable resource for researchers in the field of chemical biology and medicinal chemistry.
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[slides and audio] ZINC%3A A Free Tool to Discover Chemistry for Biology