Revised chemical component dictionary for the Worldwide Protein Data Bank

CINF 40

Muhammed Yousufuddin, myousuf@rcsb.rutgers.edu1, Dimitris Dimitropoulos2, Zukang Feng1, Jeramia Ory1, Hyunmi Sun1, John Westbrook1, Kim Henrick2, and Helen Berman1. (1) Rutgers, The State University of New Jersey, Research Collaboratory for Structural Bioinformatics Protein Data Bank, Department of Chemistry, 610 Taylor Rd, Piscataway, NJ 08854, (2) EMBL Outstation-Hinxton, MSD-EBI, Cambridge, United Kingdom
The RCSB PDB, in collaboration with the MSD-EBI, has developed and released a new and expanded chemical component dictionary. This new dictionary, which now contains around 8000 small molecules, has been improved by removing redundant ligands such as SUL, correcting any valence errors, and providing IUPAC atom labeling for standard amino acids and nucleotides. In addition, the new dictionary contains many additional data items such as stereochemical assignments, idealized coordinates, and SMILES strings.

The contents of this new chemical component dictionary have been used to remediate the entire PDB archive, which currently contains over 42,000 entries. The detailed annotation of small molecules in the archive makes greater integration with cheminformatics databases and pharmaceutical applications possible.

The wwPDB is accessible from www.wwpdb.org. We acknowledge the support of our funding agencies: RCSB PDB (NSF, NIGMS, DOE, NLM, NCI, NCRR, NIBIB, NINDS) and MSD-EBI (Wellcome Trust, EU, CCP4, BBSRC, MRC and EMBL).

 

Sci-Mix
8:00 PM-10:00 PM, Monday, August 20, 2007 BCEC -- Exhibit Hall - B2, Sci-Mix

Division of Chemical Information

The 234th ACS National Meeting, Boston, MA, August 19-23, 2007