In addition, the protein-ligand interaction patterns of the docking poses were compared to those observed in a comprehensive set of measured structural data of protein-ligand complexes of the same target protein ("reference set") using the protein-ligand interaction fingerprint (PLIF). The reference set of experimentally determined protein-ligand structures was obtained from the Protein Data Bank () with SIENA 28 using the "ligand pose comparison" mode. In ligand pose comparison mode, SIENA retrieves all measured protein-ligand complexes with backbone conformations similar to the query structures (i.e., the structures provided by DUDE-Z). The structures retrieved with SIENA were filtered for binding sites with a "binding site identity" of 1.0 (meaning that the amino acids forming the binding site of the retrieved structure are identical to those forming the binding site of the query structure). The remaining protein-ligand structures were parsed with the MDAnalysis package, and the ligand structures were extracted. Both the protein and ligand structures were protonated at pH 7.4 using OpenBabel. Subsequently, the ligands were locally minimized inside the respective binding sites with the Vina scoring function via the smina 26 interface.