Macrocyclic lead optimisation
Macrocycles are becoming increasingly popular in drug discovery, due to their vast potential against previously “undruggable” targets. But the size…
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 (>4.2 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 4-2024:
- Enamine: 4-2024 Full (File size: 119 GB)
- Enamine: 4-2024 Tenth (File size: 12 GB)
- Enamine: 4-2024 Hundredth (File size: 1.2 GB)
- Enamine: 4-2024 Thousandth (File size: 121 MB)
Using virtual screening collections in StarDrop
To start a virtual screening experiment, click the arrow button menu 
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 the StarDrop user guide.
3D molecular design resources
Conformational strain of macrocyclic peptides in ligand–receptor complexes based on advanced refinement of bound-state conformers
To better understand conformational propensities, global strain energies were estimated for 156 protein-macrocyclic peptide cocrystal structures.
3D virtual screening with Surflex eSim3D
When exploring chemistry space around a known hit or lead, you can use 3D virtual screening to identify new compounds…