A large number of example protein-protein complexes have been compiled by Zhiping Weng's ZDOCK group, and may be downloaded from the Docking Benchmark page. The following two PDB files correspond to the bound conformations of the first enzyme-inhibitor Benchmark example:
The following two PDB files correspond to the unbound conformations of the same proteins:
The above examples may be downloaded and given as the "receptor" and "ligand" input files for docking by the HexServer.
In general, PDB files may be downloaded from the RCSB Protein Data Bank. Before doing a docking calculation, it is usually a good idea to examine your PDB files using a visualisation tool such as Hex, Jmol, or VMD, and then to use a text editor to delete any duplicate domains or unwanted atoms before docking. It is also strongly recommended to study the relevant literature in order to find information about the possible interface site(s) on one or both proteins. If you can specify a possible interface residue for each protein (step 2: Docking Parameters), you can limit the angular search range, and this will greatly increase the probability of finding a high-ranking near-native prediction in the results list.