Figure 3. The retrieval index in three dimensions. One point per indexed co-crystal ligand, embedded by UMAP directly from the full 10,549-bit fingerprints under Jaccard distance, which on binary vectors is the Tanimoto coefficient retrieval uses. Nothing is reduced or compressed first, so the distances drawn here are the distances the search computes. Points are colored by the target class the ligand was solved against. Orforglipron and daraxonrasib are ringed and labeled, each joined to the indexed ligand that carried its true target. Drag to rotate, scroll to zoom. The embedding is a navigational aid; recall is measured in section 3.4.