ZINC20

ZINC20 provides an ultralarge database of commercially available small molecules for virtual screening and ligand discovery.

Key Features:

• Ultralarge-scale database: Contains over 230 million purchasable compounds in ready-to-dock 3D formats and more than 750 million purchasable compounds searchable for analogs.
• Make-on-demand compounds: Includes billions of make-on-demand molecules that expand accessible chemical space.
• Graph-based search methods: Implements explicit atomic-level graph-based searches, including SmallWorld for similarity search and Arthor for pattern and substructure search.
• 3D docking methods: Integrates 3D docking techniques to evaluate molecular interactions in a spatial context.

Scientific Applications:

• Ligand discovery and assay candidate identification: Enables identification and procurement of new small molecules for biological assays via virtual screening.
• Exploration of make-on-demand diversity: Reveals structural features absent from in-stock collections, with over 97% of core Bemis-Murcko scaffolds in make-on-demand libraries absent from existing collections.
• Scaffold expansion analysis: Documents a significant rise in new Bemis-Murcko scaffolds, correlating with an 88-fold increase in molecules compared to in-stock sets.
• Shape-space exploration: Highlights increased numbers of disc- and sphere-like shaped molecules within make-on-demand libraries compared to physical libraries.

Methodology:

Computational methods include explicit atomic-level graph-based searches (SmallWorld for similarity and Arthor for pattern/substructure), searches for analogs across purchasable compounds, and 3D docking of ready-to-dock 3D formats.