7.9 years ago by
You have got 2 choices here:
- select a large dataset from a database of small molecules, e.g. ZINC, as you suggested
- try to design a molecule to fit your binding pocket
To find suitable potential inhibitors, you can make use of the fact that an inhibitor is in most cases structurally related to the substrate. E.g., you could enter the substrate in ZINC and search for structures of 80% similarity as a basis of your virtual screening experiment.
For academically licensed docking tools, you can have a look at AutoDock or UCSF Dock.
edit: I missed the PPI here. The workflow is generally the same, but you of course don't have a substrate to start your search with. You could look for compounds structurally similar to a part of the interfacing area or do a random set of small molecules (which may not work too well).