Molecular Biotechnology

, Volume 42, Issue 1, pp 1–13

Data Deposition and Annotation at the Worldwide Protein Data Bank

  • Shuchismita Dutta
  • Kyle Burkhardt
  • Jasmine Young
  • Ganesh J. Swaminathan
  • Takanori Matsuura
  • Kim Henrick
  • Haruki Nakamura
  • Helen M. Berman
Review

Abstract

The Protein Data Bank (PDB) is the repository for three-dimensional structures of biological macromolecules, determined by experimental methods. The data in the archive is free and easily available via the Internet from any of the worldwide centers managing this global archive. These data are used by scientists, researchers, bioinformatics specialists, educators, students, and general audiences to understand biological phenomenon at a molecular level. Analysis of this structural data also inspires and facilitates new discoveries in science. This chapter describes the tools and methods currently used for deposition, processing, and release of data in the PDB. References to future enhancements are also included.

Keywords

Protein Data Bank (PDB) wwPDB Deposition Annotation Validation 

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Copyright information

© Humana Press 2008

Authors and Affiliations

  • Shuchismita Dutta
    • 1
  • Kyle Burkhardt
    • 1
    • 2
  • Jasmine Young
    • 1
  • Ganesh J. Swaminathan
    • 3
  • Takanori Matsuura
    • 4
  • Kim Henrick
    • 3
  • Haruki Nakamura
    • 4
  • Helen M. Berman
    • 1
  1. 1.Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), Department of Chemistry and Chemical BiologyRutgers, The State University of New JerseyPiscatawayUSA
  2. 2.Office of Research and Project AdministrationPrinceton UniversityPrincetonUSA
  3. 3.The Macromolecular Structure Database at the European Bioinformatics Institute PDB-eEMBL Outstation-HinxtonCambridgeUK
  4. 4.Protein Data Bank Japan (PDBj), Institute for Protein ResearchOsaka UniversitySuitaJapan

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