The database of protein-protein co-crystallized structures is built on the basis of biological unit files from PDB (Biounit files). More information about biounit and data selection can be obtained here.
Identifying associated unbound structures
Unbound structures are separate structures that are also co-crystallized in a complex. If the unbound structure is not found in PDB, it is simulated based on the bound one using Langevin dynamics simulations (Kirys et al, BMC Bioinformatics, 2015, 16:243).