ZINC — A Free Database of Commercially Available Compounds for Virtual Screening.

Abstract

A critical barrier to entry into structure-based virtual screening is the lack of a suitable, easy to access\ndatabase of purchasable compounds. We have therefore prepared a library of 727 842 molecules, each with\n3D structure, using catalogs of compounds from vendors (the size of this library continues to grow). The\nmolecules have been assigned biologically relevant protonation states and are annotated with properties\nsuch as molecular weight, calculated LogP, and number of rotatable bonds. Each molecule in the library\ncontains vendor and purchasing information and is ready for docking using a number of popular docking\nprograms. Within certain limits, the molecules are prepared in multiple protonation states and multiple\ntautomeric forms. In one format, multiple conformations are available for the molecules. This database is\navailable for free download (http://zinc.docking.org) in several common file formats including SMILES,\nmol2, 3D SDF, and DOCK flexibase format. A Web-based query tool incorporating a molecular drawing\ninterface enables the database to be searched and browsed and subsets to be created. Users can process their\nown molecules by uploading them to a server. Our hope is that this database will bring virtual screening\nlibraries to a wide community of structural biologists and medicinal chemists.