ACD Naming Software Will Be Applied to PDB Worldwide Repository of Protein Structures
September 25, 2001, Piscataway, NJ and Toronto, Canada -
Advanced Chemistry Development (ACD) and the Protein Data Bank (PDB) are proud to announce a collaboration in which ACD 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's 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's 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 Data Bank 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 Data Bank has over 16,200 protein structures and adds new structures every year.
"At RCSB, we strive to add new value to the content of the PDB. At PDB, we continually work to improve the uniformity and reliability of our structure entries, and we believe that annotating the records with accurate chemical structure names will enhance the ability of researchers to access the small molecule components in macromolecular 3D structures. We are therefore very excited to have partnered with ACD," said John Westbrook, co-director of the PDB at Rutgers University.
"ACD is proud to add this relationship to its growing portfolio of partners that recognize ACD as the definitive standard in chemical naming software. It is an honor to be working with such a well-known repository. It is also a challenge due to the size and the complex nature of some of the entries. However, we have a very active Name team, with a leader recognized by IUPAC, so we are confident that we can handle the project." said Antony Williams, Vice President of Scientific Development. "The addition of ACD/IUPAC names to the PDB will give researchers added clarity about the nature of small molecule ligands in the PDB, which are a rich source of information for those who study and employ techniques in Structure Based Drug Design."
Dr. Williams added that the PDB collaboration is sure to result in "future enhancements of interest to protein scientists."
|
