The same index the site searches, as plain text. Every co-crystal ligand in the Protein Data Bank that passes the admission rule, its pharmacophore fingerprint, and the proteins and entries it was solved against. Screen your own molecules against it on your own machine.
Every fingerprint in the index is computed by PharmCast v10 under RDKit 2025.9.6, the release this site serves, and the index is rebuilt in that same environment each week. To compare your own molecules against it, fingerprint them with rdkit ≥ 2025.9.6: RDKit computes the network's input, so an earlier release gives a different fingerprint for the same structure. pharmcast pins that floor, and pharmcast verify confirms an install reproduces the published fingerprints.