Protein Data Bank
The Protein Data Bank (PDB) is a collection of information about the three dimensional (3-D) structure of large biological molecules, such as proteins and nucleic acids. Biologists and biochemists from around the world send in the data. Most data comes from X-ray crystallography or NMR spectroscopy. Anyone can access the PDB for free online. The Worldwide Protein Data Bank, wwPDB, manages the PDB.
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| Description | Protein structure X-ray crystallography NMR Structure Determination |
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| Data format | PDB |
| Website | www |
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The PDB is useful for scientists studying structural biology and structural genomics. Many scientists have to send their information to the database. Major scientific journals and some funding agencies, such as the National Institutes of Health in the United States have rules telling scientists to send the data to the PDB. The PDB has the original or primary data. Hundreds of other databases reuse the data. These secondary databases organize the information in different ways. For example, both SCOP and CATH put structures into groups organized by type of structure and ideas about how they are related through evolution. Gene ontology puts the data into groups based on genes.[1]
References
change- ↑ Berman, H. M. (January 2008). "The Protein Data Bank: a historical perspective" (PDF). Acta Crystallographica Section A: Foundations of Crystallography. A64 (1): 88–95. doi:10.1107/S0108767307035623. PMID 18156675.
Related pages
change- Database of Molecular Motions
- The Worldwide Protein Data Bank (wwPDB) – parent site to regional hosts (below)
- RCSB Protein Data Bank (USA)
- PDBe (Europe)
- PDBj (Japan)
- BMRB, Biological Magnetic Resonance Data Bank Archived 2020-10-20 at the Wayback Machine (USA)
- wwPDB Documentation – documentation on both the PDB and PDBML file formats
- Looking at Structures Archived 2011-03-24 at the Wayback Machine – The RCSB's introduction to crystallography
- PDBsum Home Page – Extracts data from other databases about PDB structures.
- Nucleic Acid Database, NDB Archived 2021-04-17 at the Wayback Machine – a PDB mirror especially for searching for nucleic acids
- Introductory PDB tutorial sponsored by PDB Archived 2014-02-02 at the Wayback Machine