Where can I obtain ligand databases for virtual screening?

Schrödinger offers the Phase Commercially Available Compound Database (CACDB) for screening against a pharmacophore model. This is a Phase database, not a flat Maestro or SD file. However, the Virtual Screening Workflow (VSW) can take a Phase database as input, or you can extract structures and conformations via Applications → Phase → Manage Phase Database.

Beyond the Phase CACDB, Schrödinger only provides a few small ligand sets. On our Download Center, you'll find the Glide Drug-like Ligand Decoy sets, a fragment library, and the CombiGlide Diverse Side-chain Collection.

There are a number of places where you can obtain ligand structures for screening. You can download ligand catalogs in SDF format from most vendor websites (e.g., Asinex Gold or Platinum collection). Other public databases (or compilations of databases) are available from ZINC, PubChem, NCI, etc.

We recommend preparing any of these public databases with LigPrep and Epik. ZINC actually has prepared, 3D databases that used Epik for state generation, so those structures can be used directly for virtual screening (e.g., with Glide). However, for best results we still recommend LigPrep over the preparation process used for ZINC.

Keywords: Glide

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