[ricksunny]

For docking: Autodock Vina (from Scripps) is the most frequently cited docking software in the biomedical research literature. It's open source.

Researchers use docking software to run libraries of existing drugs as well as design never-seen-before drugs out of the enzyme protein's active-site pocket.

These operations have been performed extensively this year (by research groups all over the world) on covid's main protease enzyme as well as the spike-ACE2 interface, for example.