StarDrop users who have licensed the Surflex eSim3D module can freely download prepared virtual screening collections for use in StarDrop.
Enamine’s commercially available screening collection (>3.7 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.
Enamine version 3-2023:
- Enamine: 3-2023 Full (File size: 105 GB)
- Enamine: 3-2023 Tenth (File size: 10.6 GB)
- Enamine: 3-2023 Hundredth (File size: 1.1 GB)
- Enamine: 3-2023 Thousandth (File size: 106 MB)
Using virtual screening collections
To start a virtual screening experiment, click the arrow button menu 
and choose Run Virtual Screen.
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
button. - Download a PDB containing the molecule in a bioactive conformation by clicking the
button. - Use an entire bunding hypothesis or obtain a molecule in a specific conformation from a binding hypothesis result by clicking the
button. - Use a compound in the 3D Viewer by selecting all atoms of the molecule and clicking the
button.
Once the desired input conformations have been selected, click Next.
In the next page of the wizard, you can Choose a virtual screening database.
Load the virtual screen collection by clicking on 
button , locate where you saved the files and confirm it.
For more details, please refer to StarDrop 7.5 guide.