Chemical and protein structural basis for biological crosstalk between PPARα and COX enzymes
Here we present an analysis of novel drug/target predictions, focusing on those that were not obvious based on known pharmacological crosstalk.
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.
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.
Here we present an analysis of novel drug/target predictions, focusing on those that were not obvious based on known pharmacological crosstalk.
Ann and Ajay discuss the science behind and applications of the eSim molecular similarity method, a ligand-based drug design approach which considers surface-shape, electrostatics, and directionally sensitive hydrogen-bonding when comparing two molecules.
This worked example explores ways to assess and design compounds in 3D using the SeeSAR Pose module.