Compound Ranking Based on Fuzzy Three-Dimensional Similarity Improves the Performance of Docking into Homology Models of G-Protein-Coupled Receptors

[Image: see text] Ligand docking into homology models of G-protein-coupled receptors (GPCRs) is a widely used approach in computational compound screening. The generation of “double-hypothetical” models of ligand–target complexes has intrinsic accuracy limitations that further complicate compound ranking and selection compared to those of X-ray structures. Given these uncertainties, we have explored “fuzzy 3D similarity” between hypothetical binding modes of known ligands in homology models and docking poses of database compounds as an alternative to conventional scoring schemes. Therefore, GPCR homology models at varying accuracy levels were generated and used for docking. Increases in recall performance were observed for fuzzy 3D similarity ranking using single or multiple ligand poses compared to that of conventional scoring functions and interaction fingerprints. Fuzzy similarity ranking was also successfully applied to docking into an external model of a GPCR for which no experimental structure is currently available. Taken together, our results indicate that the use of putative ligand poses, albeit approximate at best, increases the odds of identifying active compounds in docking screens of GPCR homology models.