The G-protein coupled receptor (GPCR) superfamily is currently the largest class of therapeutic targets. In silico prediction of interactions between GPCRs and small molecules in the transmembrane ligand-binding site is therefore a crucial step in the drug discovery process, which remains a daunting task due to the difficulty to characterize the 3D structure of most GPCRs, and to the limited amount of known ligands for some members of the superfamily. Chemogenomics, which attempts to characterize interactions between all members of a target class and all small molecules simultaneously, has recently been proposed as an interesting alternative to traditional docking or ligand-based virtual screening strategies.