A pivotal step in the drug discovery process is quantifying the interaction of a compound with a protein target of interest. For this purpose, many different biological assays have been developed that quantify these interactions in systems ranging from (radio)ligand binding assays on cell membranes to functional downstream effects in cellular systems. To capture structure activity relationships in the data gathered by these assays, protein-ligand interaction models have proven to be useful. These in silico methods allow for the identification of compounds with a desired predicted interaction profile and they can increase the efficiency of the drug discovery process. This can be used to enrich for compounds with a high potency on a drug target or with minimal interactions that cause side-effects.