Structure based ligand discovery
Structure based ligand discovery is the use of a macromolecular (usually protein) structure to discover new liggands. At a high level, there are three ways to go about this:
1. have an expert look at the model, and draw a molecule that complements the binding site. 2. Perform #1 using an automatic program. This is called denovo design. 3. Dock a database of small molecules into the binding site, and rank them from best to worst.
The problem with method #1 is that it is very labor intensive, and that any compound invented may be difficult and/or expensive to make. The problem with approach #2 is that the compounds may still be difficult to acquire, although there are strategies to overcome this limitations. It can also be, relatively speaking, slow.