Advanced Chemistry Development and the Protein Data Bank

Advanced Chemistry Development (ACD/Labs) and the Protein Data Bank (PDB) are proud to announce a collaboration in which ACD/Labs will provide their naming software product ACD/Name to the PDB for use in its data processing and annotation operations. The algorithms in ACD/Name allow rapid systematic chemical naming according to the International Union of Pure and Applied Chemistry (IUPAC) Recommendations on Nomenclature of Organic Chemistry (1979 and 1993) for almost any organic structure, as well as selected classes of biochemical, organometallic, and inorganic structures.

Recent improvements to ACD/Name are diverse and include the ability to handle spiro compounds with polycyclic components; a-amino acids; peptides and their derivatives; assemblies of cyclic systems; bridged fused systems; and polysaccharides. The PDB has agreed to add systematic names of small molecules to the Data Bank by using ACD/Labs' Name algorithm. Due to the size of the PDB and the complexity of the structures, the Name algorithm will be provided to the PDB in the form of ACD/Labs' IUPAC Name Batch software, capable of running on the SGI platform. This collaboration will aid researchers by providing unequivocal names for the co-factors and ligands bound to macromolecules with the entries of the PDB.

The PDB is the authoritative worldwide data repository for the processing and distribution of 3-D biological macromolecular structure data and protein crystal structures, dating back to the very first structures ever solved by x-ray diffraction. It is a vital resource for all aspects of structural biology and modern techniques in drug discovery. In recent years, the Protein Databank has come under the progressive leadership of the Research Collaboratory for Structural Biology, a collaboration between Rutgers University's Department of Chemistry, the San Diego Supercomputer Center, and NIST (National Institute of Standards and Technology). Currently, the Databank has over 16,200 protein structures and adds new structures every year.

PDB and ACD/Labs press release