StarDrop users who have licensed the Surflex eSim3D module can freely download prepared virtual screening collections for use in StarDrop.
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.
The eMolecules collection has around 10 million compounds. Because of its size, we split the files into batches, which can be catenated, once they are downloaded. Alternatively, you could run the screen on each batch, then merge the results into a single file, then focus on the highest scoring results. If you need any help, please don’t hesitate to reach to our support team.
These collections will be updated regularly.
eMolecule version 9-2023:
- eMolecule batch 00: 9-2023 (File size: 103 GB)
- eMolecule batch 01: 9-2023 (File size: 120 GB)
- eMolecule batch 02: 9-2023 (File size: 118 GB)
- eMolecule batch 03: 9-2023 (File size: 108 GB)
- eMolecule batch 04: 9-2023 (File size: 108 GB)
- eMolecule: 9-2023 Tenth (File size: 55.4 GB)
- eMolecule: 9-2023 Hundredth (File size: 5.5 GB)
- eMolecule: 9-2023 Thousandth (File size: 557 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.