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| About John Westbrook (Rutgers) |
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John Westbrook is an Associate Research Professor in the Department of Chemistry and Chemical Biology at Rutgers, The State University of New Jersey, where he works on the RCSB Protein Data Bank (www.pdb.org) and the PSI Structural Genomics Knowledgebase projects
(kb.psi-structuralgenomics.org). He is involved in the architectural design of the systems that support these resources, including deposition, annotation, and distribution. Dr. Westbrook was the leader in the development of the macromolecular Crystallographic Information File, and remains very active in community discussions of data format issues.
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Small Molecule Data in the Protein Data Bank Archive
John Westbrook (1), Kim Henrick (2), and Dimitris Dimitropoulos (2)
(1) RCSB Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
(2) PDBe, EMBL - European Bioinformatics Institute, Hinxton, Cambridge, UK
The Protein Data Bank archive contains over 8350 unique chemical components. These chemical components are described in a data dictionary maintained by the Worldwide Protein Data Bank (wwPDB; wwpdb.org). In 2007, the wwPDB Chemical Component Dictionary was extended to include IUPAC atom nomenclature for standard amino acids and nucleotides, stereochemical assignments, aromatic bond assignments, experimental model and computed ideal coordinates, systematic names and chemical descriptors. Some improved web tools which take advantage
of the more detailed chemical descriptions and assist users in finding small molecules in the PDB will be described.
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