Knowledge Base

Where can I obtain ligand databases for virtual screening?

Schrödinger has partnered with Enamine, MilliporeSigma, and MolPort to provide a Phase database of fragments, lead-like, near drug-like, and drug-like compounds available from Enamine's “Stock Screening Compounds Collection”, MilliporeSigma's “Aldrich Market Select”, and MolPort's “Screening Compound Database” respectively.

The Phase databases can be used as input for both Glide and the Virtual Screening Workflow (VSW), as well as for Shape Screening and the pharmacophore-based Ligand Screening. Structures and conformers can be extracted from the Phase database, using the Manage Phase Database panel.

You can find more information about the three databases from the Phase product page.

The databases are large (100s of GB) but depending on your internet download speed and database selection they can be made available for download. If you are interested in obtaining the Enamine, MilliporeSigma, or MolPort databases, please contact your account manager or

Beyond the above-mentioned databases, Schrödinger only provides a few small ligand sets. In the Download Center, you'll find the Glide Drug-like Ligand Decoy sets and the CombiGlide Diverse Side-chain Collection. A fragment library is also available, and it is shipped together with our software.

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 the best results, we still recommend LigPrep over the preparation process used for ZINC.

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