ACDLabs: ACD/Name is a tool that generates chemical names from structure according to IUPAC rules. ACD/Name can also convert chemical names to structures. ACD/Name handles challenging areas of nomenclature including biochemical, inorganic, and organometallic structures and polymers. RCSB PDB uses ACD/Name to generate chemical names for each of the molecules in the Chemical Component Dictionary.

Cambridge Crystallographic Data Centre: RCSB PDB uses CCDC software to generate chemical component matching between the CSD and PDB archives and the ligand quality displays on RCSB.org.

ChemAxon: RCSB PDB uses the web-based chemical drawing tool Marvin JS to compose chemical sketches for chemical similar and substructure searches.

OpenEye, Cadence Molecular Sciences: The OpenEye cheminformatics suite of toolkits including: OEChem TK, core chemistry handling and representation; OEDepict TK, 2D Molecule rendering and depiction; MolProp TK, molecular property calculation and filtering; and Quacpac TK, tautomer enumeration and charge assignment. RCSB PDB uses OpenEye toolkits for image generation and searching small molecule constituents in PDB entries.