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Protein Data Bank

Protein Data Bank
Content
Description
Contact
Primary citationPMID 30357364
Access
Data formatmmCIF, PDB
Website

The Protein Data Bank (PDB)[1] is a database for the three-dimensional structural data of large biological molecules such as proteins and nucleic acids, which is overseen by the Worldwide Protein Data Bank (wwPDB). These structural data are obtained and deposited by biologists and biochemists worldwide through the use of experimental methodologies such as X-ray crystallography, NMR spectroscopy, and, increasingly, cryo-electron microscopy. All submitted data are reviewed by expert biocurators and, once approved, are made freely available on the Internet under the CC0 Public Domain Dedication.[2] Global access to the data is provided by the websites of the wwPDB member organisations (PDBe,[3] PDBj,[4] RCSB PDB,[5] and BMRB[6]).

The PDB is a key in areas of structural biology, such as structural genomics. Most major scientific journals and some funding agencies now require scientists to submit their structure data to the PDB. Many other databases use protein structures deposited in the PDB. For example, SCOP and CATH classify protein structures, while PDBsum provides a graphic overview of PDB entries using information from other sources, such as Gene Ontology.[7][8]

  1. ^ wwPDB, Consortium (2019). "Protein Data Bank: the single global archive for 3D macromolecular structure data". Nucleic Acids Res. 47 (D1): 520–528. doi:10.1093/nar/gky949. PMC 6324056. PMID 30357364.
  2. ^ wwPDB.org. "wwPDB: Usage Policies". www.wwpdb.org. Retrieved 2024-04-16.
  3. ^ "PDBe home < Node < EMBL-EBI". pdbe.org.
  4. ^ "Protein Data Bank Japan – PDB Japan – PDBj". pdbj.org.
  5. ^ Bank, RCSB Protein Data. "RCSB PDB: Homepage". rcsb.org.
  6. ^ Cite error: The named reference :0 was invoked but never defined (see the help page).
  7. ^ Berman, H. M. (January 2008). "The Protein Data Bank: a historical perspective" (PDF). Acta Crystallographica Section A. A64 (1): 88–95. doi:10.1107/S0108767307035623. PMID 18156675.
  8. ^ Laskowski RA, Hutchinson EG, Michie AD, Wallace AC, Jones ML, Thornton JM (December 1997). "PDBsum: a Web-based database of summaries and analyses of all PDB structures". Trends Biochem. Sci. 22 (12): 488–90. doi:10.1016/S0968-0004(97)01140-7. PMID 9433130.