Protein Data Bank

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Examples of protein structures from the PDB

The Protein Data Bank ( PDB ) is an open access database for 3D structural data of large biological molecules. Via an internet information portal and a downloadable data archive, the PDB offers access to 3D structural data for ( proteins , DNA and RNA ). Today it is a leading global resource for experimental data, which is central to scientific discoveries. Knowing the 3D structure of a biological macromolecule is essential for understanding its function. The structural data were usually obtained by crystal structure analysis or NMR spectroscopy .

The archive of the protein database (PDB) currently contains over 158,000 entries (as of 2019) as 3D structures of biomolecules at the atomic level.

The PDB was set up in 1971 as the first freely accessible digital data source in biology and the data centers are operated by the Research Collaboratory for Structural Bioinformatics (RCSB PDB). It provides PDB data to all data consumers free of charge and without usage restrictions (policies).

The RCSB-PDB is operated at Rutgers, the State University of New Jersey and the University of California San Diego / San Diego SupercomputerCenter. Through a unique agreement, PDB data is also made available by other partners of the Worldwide Protein Data Bank (including Protein Data Bank Europe (PDBe)), Protein Data Bank Japan and the Biological Magnetic Resonance Bank. However, the RCSB-PDB team (which works at Rutgers University and the University of CaliforniaSan Diego) is the wwPDB archive maintainer and is also responsible for data integrity and disaster recovery. The total cost of ownership for the RCSB-PDB, including data creation, storage and other expenses, is $ 6.9 million per year.

history

PDB originally consisted of protein structures from X-ray crystal structure analysis and the Brookhaven RAster Display (BRAD) founded in 1968 . The BRAD system was able to draw digitized images from Hough Powell bubble chamber photographs onto a black and white television monitor. The developers of the BRAD system recognized the potential of the BRAD system for 3D graphics and Dr. Walter C. Hamilton, chief chemist at Brookhaven National Laboratory , used the potential of the BRAD display for 3D molecular graphics. Together with Edgar Meyer ( Texas A&M University ) the program DISPLAY , a software for storing atomic coordinates in a common format, was introduced. The DISPLAY program could draw 3D models with up to 512 atoms.

Until 1970, the available atomic coordinates of proteins were collected in Brookhaven and saved in a standardized format using the PROIN program. Because of the limited access to graphical representations, they were rarely used widely; one could only admire endless lists of atomic coordinates or bend brass rods to look like fossilized earthworms. Therefore, Meyer's SEARCH program was written in FORTRAN in 1971 to access the PDB and provide coordinates for offline display. It could select a specific protein from the PDB and extract atomic coordinates based on atomic type, residue type, or sequence range. After Hamilton's death in 1973, Tom Koeztle took over the management for the next 20 years. In 1994 the management passed to Joel Sussman .

From October 1998 to June 1999, PDB was transferred to the Research Collaboratory for Structural Bioinformatics (RCSB). There Helen M. Berman of Rutgers University became the new director. In 2003 PDB went international with the creation of Worldwide Protein Data Bank (wwPDB). Founding members are PDBe (Europe), RCSB (USA) and PDBj (Japan). In 2006 the Biological Magnetic Resonance Bank (BMRB) joined. Each entry is processed by the employees.

See also

literature

Web links

Individual evidence

  1. ↑ PDB Statistics: Overall Growth of Released Structures Per Year. Retrieved August 19, 2020 .
  2. ↑ Kevin P. Sullivan, Peggy Brennan-Tonetta, Lucas J. Marxen: Economic Impacts of the Research Collaboratory for Structural Bioinformatics (RCSB) Protein Data Bank. Rutgers New Jersey Agricultural Experiment Station, 2017, accessed August 19, 2020 .
  3. ^ A b EF Meyer: The first years of the Protein Data Bank . In: Cambridge University Press (Ed.): Protein Science . 6, No. 7, 1997, pp. 1591-1597. doi : 10.1002 / pro.5560060724 . PMID 9232661 . PMC 2143743 (free full text).
  4. ↑ RCSB / Research Collaboratory for Structural Bioinformatics ( Memento of the original from February 5, 2007 in the Internet Archive ) Info: The archive link was automatically inserted and not yet checked. Please check the original and archive link according to the instructions and then remove this notice. @1@ 2Template: Webachiv / IABot / home.rcsb.org
  5. ↑ HM Berman, J Westbrook, Z Feng, G Gilliland, TN Bhat, H Weissig, IN Shindyalov, PE Bourne: The Protein Data Bank . In: Nucleic Acids Res . 28, No. 1, January 2000, pp. 235-242. doi : 10.1093 / nar / 28.1.235 . PMID 10592235 . PMC 102472 (free full text).
  6. ↑ RCSB PDB Newsletter Archive . RCSB Protein Data Bank.
  7. ↑ PDBE Protein Data Bank in Europe
  8. ↑ Welcome to PDBj
  9. ↑ BMRB / Biological Magnetic Resonance Bank
  10. ^ E Curry, A Freitas, S O'Riáin: The Role of Community-Driven Data Curation for Enterprises . In: D. Wood (Ed.): Linking Enterprise Data . Springer US, Boston MA 2010, ISBN 978-1-4419-7664-2 , pp. 25-47.
  11. ↑ PDB Validation Suite