StarDrop users who have licensed the Surflex eSim3D module can freely download prepared virtual screening collections for use in StarDrop.

MolPort’s commercially available screening collection (>5 million compounds) has been prepared for use in ligand-based virtual screening. During preparation, each of the compounds has had conformations generated and stored in a *.sfdb file, which is a file format native to Surflex eSim3D. When a virtual screen is launched from StarDrop, the user points to one of these SFDB files; each conformation is aligned and scored against the reference compound, which is held in a fixed conformation.

For users wishing to run ligand-based virtual screening within StarDrop, we have made the SFDBs available for download, however, please note that the full collection file is very large and will take time to download. The full collection has been randomly split into subsets representing 1/10, 1/100, and 1/1000 of the full collection; these smaller files are also available below.

These collections will be updated regularly.

MolPort version 5-2024:

Using virtual screening collections in StarDrop

To start a virtual screening experiment, click the arrow button menu  Arrow button Run Virtual Screen.

Virtual Screen in Surflex esim

Several options are available to load the 3D input structure(s) to use for virtual screening:

Open a file containing the 3D coordinates by clicking the Open button button.
Download a PDB containing the molecule in a bioactive conformation by clicking the Download button button.
Use an entire bunding hypothesis or obtain a molecule in a specific conformation from a binding hypothesis result by clicking the Compare button button.
Use a compound in the 3D Viewer by selecting all atoms of the molecule and clicking the Arrow buttonbutton.
Once the desired input conformations have been selected, click Next.

In the next page of the wizard, you can Choose a virtual screening database.

Virtual Screening Snamine screen

Load the virtual screen collection by clicking on Find button button, locate where you saved the files and confirm it.

For more details, please refer to the StarDrop user guide.

3D molecular design resources