Suppose if there are two molecules we can predict how well one can molecule can bind to another molecule to form a stable complex (Something like Methane with Alcohol to form Methly alcholol for an example)
In Drug discovery, The interaction between a ligand (small molecule) and a protein (Virus protein) may result in inhibition of the enzyme which has the protein.That’s why compounds are docked against protein receptors (Virus protein receptors for docking)