A frequently overlooked aspect when analyzing protein structures is the crystal contacts due to the crystal lattice. Discovery Studio offers a protocol for this: the ‘Analyze Crystal Contacts’ protocol builds a shell of symmetry related copies around the asymmetric unit of a crystal structure and analyzes contacts and interactions. 

Upon running the protocol, you'll receive an output detailing contacts with adjacent protein units in the lattice. For instance, if you load TEM-1 beta-lactamase protein (PDB1PZP) into Discovery Studio, you'll observe that the protein is bound to an allosteric inhibitor. Running the "Analyze Crystal Contacts" protocol on this system will reveal that the ligand has contacts with the neighboring protein unit, potentially stabilizing its presence in the allosteric pocket.