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.
Following the paper? The frozen benchmark is a separate, dated download: the archived benchmark, index snapshot 2026-09-08.
It holds the 3,000 queries with the draw seed and rule, the ground truth map, the 10,588 generic scaffold groups, both holdout rules and both pairing maps as data, the 38 complex redocking records with their preparation logs and search boxes, the evaluation scripts, the frozen index itself and a user manual. It is pinned to 27,797 ligands and 28,579 target sites and is never rewritten, so it is not the current index: the bundle below is. Use the archive to check a published number and the bundle to screen a molecule.