Crystallography has given us the positions of atoms in crystals for 100 years, but nano-particles require a radical rethink in approach. They form interesting non-space-filling structures that we want to synthesize and control for advanced devices, but how to accurately determine the 3D atomic arrangements? Taking inspiration from genomics-based data-mining approaches, we showed how large databases of candidate structures can be generated algorithmically and then mined efficiently and robustly to screen for candidate nanoparticle structures.