John Westbrook

Summary

Affiliation: Rutgers University
Country: USA

Publications

  1. pmc The Protein Data Bank: unifying the archive
    John Westbrook
    Rutgers, The State University of New Jersey, Department of Chemistry, 610 Taylor Road, Piscataway, NJ 08854 8087, USA
    Nucleic Acids Res 30:245-8. 2002
  2. ncbi request reprint Design of a data model for developing laboratory information management and analysis systems for protein production
    Anne Pajon
    EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
    Proteins 58:278-84. 2005
  3. ncbi request reprint STAR/mmCIF: an ontology for macromolecular structure
    J D Westbrook
    Rutgers, State University of New Jersey, Department of Chemistry, Piscataway 08854 8087, USA
    Bioinformatics 16:159-68. 2000
  4. ncbi request reprint PDBML: the representation of archival macromolecular structure data in XML
    John Westbrook
    Research Collaboratory for Structural Bioinformatics Protein Data Bank RCSB PDB, Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey 610 Taylor Road, Piscataway, NJ 08854, USA
    Bioinformatics 21:988-92. 2005
  5. ncbi request reprint Ligand Depot: a data warehouse for ligands bound to macromolecules
    Zukang Feng
    Protein Data Bank, Research Collaboratory for Structural Bioinformatics, Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854, USA
    Bioinformatics 20:2153-5. 2004
  6. ncbi request reprint TargetDB: a target registration database for structural genomics projects
    Li Chen
    Research Collaboratory for Structural Bioinformatics, Protein Data Bank, Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854, USA
    Bioinformatics 20:2860-2. 2004
  7. pmc The RCSB PDB information portal for structural genomics
    Andrei Kouranov
    Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854 8087, USA
    Nucleic Acids Res 34:D302-5. 2006
  8. pmc Tools for the automatic identification and classification of RNA base pairs
    Huanwang Yang
    Department of Chemistry and Chemical Biology, Rutgers University, NJ 08854 8087, USA
    Nucleic Acids Res 31:3450-60. 2003
  9. pmc The Nucleic Acid Database: new features and capabilities
    Buvaneswari Coimbatore Narayanan
    Department of Chemistry and Chemical Biology, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, 174 Frelinghuysen Road, Piscataway, NJ 08854 8076, USA, Department of Chemistry and Center for Biomolecular Sciences, Bowling Green State University, Bowling Green, OH 43403, USA and Department of Mathematics and Statistics, Bowling Green State University, Bowling Green, OH 43403, USA
    Nucleic Acids Res 42:D114-22. 2014
  10. ncbi request reprint The nucleic acid database
    Helen M Berman
    Department of Chemistry, Rutgers University, Piscataway, NJ, USA
    Methods Biochem Anal 44:199-216. 2003

Collaborators

Detail Information

Publications26

  1. pmc The Protein Data Bank: unifying the archive
    John Westbrook
    Rutgers, The State University of New Jersey, Department of Chemistry, 610 Taylor Road, Piscataway, NJ 08854 8087, USA
    Nucleic Acids Res 30:245-8. 2002
    ..rcsb.org/pub/pdb/uniformity/data/mmCIF/). A utility application that converts the mmCIF data files to the PDB format (called CIFTr) has also been released to provide support for existing software...
  2. ncbi request reprint Design of a data model for developing laboratory information management and analysis systems for protein production
    Anne Pajon
    EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
    Proteins 58:278-84. 2005
    ..The model is described in Unified Modeling Language (UML). In addition, we present relational database schemas derived from the UML. These relational schemas are already in use in a number of data management projects...
  3. ncbi request reprint STAR/mmCIF: an ontology for macromolecular structure
    J D Westbrook
    Rutgers, State University of New Jersey, Department of Chemistry, Piscataway 08854 8087, USA
    Bioinformatics 16:159-68. 2000
    ..While the description of macromolecular structure and the x-ray crystallographic experiment used to derive it represent explicit data, the ontology is extensible and applicable to other less well-characterized data domains...
  4. ncbi request reprint PDBML: the representation of archival macromolecular structure data in XML
    John Westbrook
    Research Collaboratory for Structural Bioinformatics Protein Data Bank RCSB PDB, Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey 610 Taylor Road, Piscataway, NJ 08854, USA
    Bioinformatics 21:988-92. 2005
    ..The correspondences between the PDB dictionary and the XML schema metadata are described as well as the XML representations of PDB dictionaries and data files...
  5. ncbi request reprint Ligand Depot: a data warehouse for ligands bound to macromolecules
    Zukang Feng
    Protein Data Bank, Research Collaboratory for Structural Bioinformatics, Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854, USA
    Bioinformatics 20:2153-5. 2004
    ..rutgers.edu/. Version 1.0 supports multiple operating systems including Windows, Unix, Linux and the Macintosh operating system. The current drawing tool works in Internet Explorer, Netscape and Mozilla on Windows, Unix and Linux...
  6. ncbi request reprint TargetDB: a target registration database for structural genomics projects
    Li Chen
    Research Collaboratory for Structural Bioinformatics, Protein Data Bank, Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854, USA
    Bioinformatics 20:2860-2. 2004
    ..AVAILABILITY: TargetDB is available at http://targetdb.pdb.org/..
  7. pmc The RCSB PDB information portal for structural genomics
    Andrei Kouranov
    Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854 8087, USA
    Nucleic Acids Res 34:D302-5. 2006
    ..Functional coverage can be examined according to enzyme classification, gene ontology (biological process, cell component and molecular function) and disease...
  8. pmc Tools for the automatic identification and classification of RNA base pairs
    Huanwang Yang
    Department of Chemistry and Chemical Biology, Rutgers University, NJ 08854 8087, USA
    Nucleic Acids Res 31:3450-60. 2003
    ..rutgers.edu/services/. The application RNAMLview can also be downloaded from this site. The 2D diagrams produced by RNAview are available for RNA structures in the Nucleic Acid Database (NDB) at http://ndbserver.rutgers.edu/atlas/...
  9. pmc The Nucleic Acid Database: new features and capabilities
    Buvaneswari Coimbatore Narayanan
    Department of Chemistry and Chemical Biology, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, 174 Frelinghuysen Road, Piscataway, NJ 08854 8076, USA, Department of Chemistry and Center for Biomolecular Sciences, Bowling Green State University, Bowling Green, OH 43403, USA and Department of Mathematics and Statistics, Bowling Green State University, Bowling Green, OH 43403, USA
    Nucleic Acids Res 42:D114-22. 2014
    ..This article describes the recent redesign of the NDB Web site with special emphasis on new RNA-derived data and annotations and their implementation and integration into the search capabilities. ..
  10. ncbi request reprint The nucleic acid database
    Helen M Berman
    Department of Chemistry, Rutgers University, Piscataway, NJ, USA
    Methods Biochem Anal 44:199-216. 2003
  11. ncbi request reprint The Nucleic Acid Database
    Helen M Berman
    Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854 8087, USA
    Acta Crystallogr D Biol Crystallogr 58:889-98. 2002
    ..The architecture and capabilities of the Nucleic Acid Database, as well as some of the research enabled by this resource, are presented in this article...
  12. pmc The Protein Data Bank and structural genomics
    John Westbrook
    Research Collaboratory for Structural Bioinformatics, Rutgers, The State University of New Jersey, Department of Chemistry and Chemical Biology, 610 Taylor Road, Piscataway, NJ 08854 8087, USA
    Nucleic Acids Res 31:489-91. 2003
    ....
  13. ncbi request reprint Validation of protein structures for protein data bank
    John Westbrook
    Department of Chemistry, Rutgers State University of New York, Piscataway, New Jersey 08854, USA
    Methods Enzymol 374:370-85. 2003
  14. pmc Chemical annotation of small and peptide-like molecules at the Protein Data Bank
    Jasmine Y Young
    Department of Chemistry and Chemical Biology, and Center for Integrative Proteomics Research, Rutgers The State University of New Jersey, 174 Frelinghuysen Rd, Piscataway, NJ 08854 8087, USA and San Diego Supercomputer Centre and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093 0743, USA
    Database (Oxford) 2013:bat079. 2013
    ..Benchmark studies have shown that the Chemical Component Annotation Tool provides significant improvements in processing efficiency and data quality. Database URL: http://wwpdb.org. ..
  15. pmc Improving the representation of peptide-like inhibitor and antibiotic molecules in the Protein Data Bank
    Shuchismita Dutta
    RCSB Protein Data Bank, Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854 8076
    Biopolymers 101:659-68. 2014
    ..2013 Wiley Periodicals, Inc. Biopolymers 101: 659-668, 2014. ..
  16. ncbi request reprint The need for dictionaries, ontologies, and controlled vocabularies
    Helen M Berman
    Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, USA
    OMICS 7:9-10. 2003
  17. pmc The distribution and query systems of the RCSB Protein Data Bank
    Philip E Bourne
    San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093 0505, USA
    Nucleic Acids Res 32:D223-5. 2004
    ..The PDB's mandate is to disseminate this information in the most usable form and as widely as possible. The current query and distribution system is described and an alpha version of the future re-engineered system introduced...
  18. pmc Remediation of the protein data bank archive
    Kim Henrick
    MSD EBI, EMBL Outstation Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 36:D426-33. 2008
    ..The scope and methods used in this project are presented...
  19. ncbi request reprint Realism about PDB
    Helen M Berman
    Nat Biotechnol 25:845-6; author reply 846. 2007
  20. ncbi request reprint The Protein Data Bank and lessons in data management
    Philip E Bourne
    Department of Pharmacology and San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093 0537, USA
    Brief Bioinform 5:23-30. 2004
    ..The role of the human factor in the form of users, collaborators, scientific society and ad hoc committees is also included...
  21. ncbi request reprint A framework for scientific data modeling and automated software development
    Rasmus H Fogh
    Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
    Bioinformatics 21:1678-84. 2005
    ..The problem lies not only in defining and maintaining the standards, but also in convincing scientists and application programmers with a wide variety of backgrounds and interests to adhere to them...
  22. pmc The RCSB Protein Data Bank: a redesigned query system and relational database based on the mmCIF schema
    Nita Deshpande
    San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
    Nucleic Acids Res 33:D233-7. 2005
    ..The current capabilities of the re-engineered site, which will become the RCSB production site at http://www.pdb.org in late 2005, are described...
  23. pmc RNA backbone: consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution)
    Jane S Richardson
    Department of Biochemistry, Duke University Medical Center, Durham, North Carolina, 27710 3711, USA
    RNA 14:465-81. 2008
    ..The RNA Ontology Consortium will combine this new backbone system with others that define base pairs, base-stacking, and hydrogen-bond relationships to provide a full description of RNA structural motifs...
  24. ncbi request reprint A biologist's guide to synchrotron facilities: the BioSync web resource
    Anne Kuller
    San Diego Supercomputer Center, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093 0505, USA
    Trends Biochem Sci 27:213-5. 2002
    ..The site automatically provides timely and accurate information in a unified format by gathering technical descriptions of synchrotron beamlines using modern information management practices...
  25. pmc RNAML: a standard syntax for exchanging RNA information
    Allison Waugh
    Stanford Medical Informatics, Stanford University Medical Center, California 94305, USA
    RNA 8:707-17. 2002
    ..In addition to the various generic packages that exist to read and interpret XML formats, an XML processor was developed and put in the open-source MC-Core library for nucleic acid and protein structure computer manipulation...
  26. ncbi request reprint The CCPN project: an interim report on a data model for the NMR community
    Rasmus Fogh
    Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
    Nat Struct Biol 9:416-8. 2002
    ..A recent workshop discusses the progress toward integrating NMR data into a unifying data model...