RCSB PDB gratefully acknowledges access and support for software tools from:
- 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.
- ChemAxon: RCSB PDB uses the web-based chemical drawing tool Marvin JS to compose chemical sketches for chemical similar and substructure searches.
- OpenEye Scientific: 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 processing and searching small molecule constituents in PDB entries.
RCSB PDB would also like to acknowledge the many open source tools that are used in the production and delivery of the website. Some of the major open-source tools used include:
RCSB PDB integrates Data From External Resources for searching and analysis.
A list of software programs used by the wwPDB during OneDep deposition and validation is available.