Figure 5.

Schematic representation of three test cases, from simple to complex, in which the reference structure was used to place the ligand(s) in the target structure by GLR. The triangles labeled A and B represent protein molecules in the asymmetric unit. The black spheres and triangle with white dots represent ligands in the reference structures. The white spheres and triangles with black dots represent ligands in the target structures. In case 3 triangles rather than spheres were used to represent the ligands because when an asymmetric ligand is bound in an active site shared across a homomeric interface, an issue of directionality arises. The lower triangle associated with the target structure indicates the presence of an alternate ligand conformation with the reverse orientation.