Protein Data Bank
The Protein Data Bank (PDB) is a repository for the three-dimensional structural data of large biological molecules, such as Worldwide Protein Data Bank, wwPDB.
The PDB is a key resource 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. If the contents of the PDB are thought of as primary data, then there are hundreds of derived (i.e., secondary) databases that categorize the data differently. For example, both SCOP and CATH categorize structures according to type of structure and assumed evolutionary relations; GO categorize structures based on genes.
- History 1
- Contents 2
- Growth trend 3
- File format 4
- Viewing the data 5
- See also 6
- References 7
- External links 8
Two forces converged to initiate the PDB: 1) a small but growing collection of sets of protein structure data determined by X-ray diffraction; and 2) the newly available (1968) molecular graphics display, the Brookhaven RAster Display (BRAD), to visualize these protein structures in 3-D. In 1969, with the sponsorship of Walter Hamilton at the Brookhaven National Laboratory, Edgar Meyer (Texas A&M University) began to write software to store atomic coordinate files in a common format to make them available for geometric and graphical evaluation. By 1971, one of Meyer's programs, SEARCH, enabled researchers to remotely access information from the database to study protein structures offline. SEARCH was instrumental in enabling networking, thus marking the functional beginning of the PDB.
Upon Hamilton's death in 1973, Tom Koeztle took over direction of the PDB for the subsequent 20 years. In January 1994,
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 (USA)
- wwPDB Documentation — documentation on both the PDB and PDBML file formats
- Looking at Structures — The RCSB's introduction to crystallography
- PDBsum Home Page — Extracts data from other databases about PDB structures.
- Nucleic Acid Database, NDB — a PDB mirror especially for searching for nucleic acids
- Introductory PDB tutorial sponsored by PDB
- PDBe: Quick Tour on EBI Train OnLine
- PDBe Protein Data Bank in Europe
- Welcome to PDBj - Home
- Berman, H. M. (January 2008). "The Protein Data Bank: a historical perspective". Acta Crystallographica Section A: Foundations of Crystallography A64 (1): 88–95.
- Meyer EF (1997). "The first years of the Protein Data Bank". Protein Science (Cambridge University Press) 6 (7): 1591–1597.
- Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE (January 2000). "The Protein Data Bank". Nucleic Acids Res. 28 (1): 235–242.
- RCSB | Research Collaboratory for Structural Bioinformatics
- "RCSB PDB Newsletter Archive". RCSB Protein Data Bank.
- BMRB - Biological Magnetic Resonance Bank
- Curry E, Freitas A, O'Riáin S (2010). "The Role of Community-Driven Data Curation for Enterprises". In D. Wood. Linking Enterprise Data. Boston, MA: Springer US. pp. 25–47.
- PDB Validation Suite
- "PDB Current Holdings Breakdown". RCSB.
- "The Uppsala Electron Density Server". Uppsala University. Retrieved 2013-04-06.
- Kleywegt GJ, Harris MR, Zou JY, Taylor TC, Wählby A, Jones TA (Dec 2004). "The Uppsala Electron-Density Server". Acta Crystallogr D Biol Crystallogr 60 (Pt 12 Pt 1): 2240–2249.
- Anon (2014). "Hard data: It has been no small feat for the Protein Data Bank to stay relevant for 100,000 structures". Nature 509 (7500): 260.
- "Content Growth Report". RCSB PDB. Retrieved 2013-04-06.
- Westbrook J, Ito N, Nakamura H, Henrick K, Berman HM (April 2005). "PDBML: the representation of archival macromolecular structure data in XML". Bioinformatics 21 (7): 988–992.
- "ICM-Browser". Molsoft L.L.C. Retrieved 2013-04-06.
- "Swiss PDB Viewer".
- STAR: Biochem - Home
- "VisProt3DS". Molecular Systems Ltd. Retrieved 2013-04-06.
- Crystallographic database
- Protein structure
- Protein structure prediction
- Protein structure database
- PDBREPORT lists all anomalies (also errors) in PDB structures
- PDBsum — extracts data from other databases about PDB structures
- PDBWiki — a website for community annotation of PDB structures
- Proteopedia — a collaborative 3D encyclopedia of proteins and other molecules
The structure files may be viewed using one of several open source computer programs. Some other free, but not open source programs include ICM-Browser, VMD, MDL Chime, Pymol, UCSF Chimera, Rasmol, Swiss-PDB Viewer, StarBiochem (a Java-based interactive molecular viewer with integrated search of protein databank), Sirius, and VisProt3DS (a tool for Protein Visualization in 3D stereoscopic view in anaglyth and other modes). The RCSB PDB website contains an extensive list of both free and commercial molecule visualization programs and web browser plugins.
Viewing the data
4hhb" is the PDB identifier. Each structure published in PDB receives a four-character alphanumeric identifier, its PDB ID. (This cannot be used as an identifier for biomolecules, because often several structures for the same molecule—in different environments or conformations—are contained in PDB with different PDB IDs.)
For PDB format files, use, e.g.,
http://www.pdb.org/pdb/files/4hhb.pdb.gz or http://pdbe.org/download/4hhb
For PDBML (XML) files, use, e.g.,
http://www.pdb.org/pdb/files/4hhb.xml.gz or http://pdbe.org/pdbml/4hhb
The file format initially used by the PDB was called the PDB file format. This original format was restricted by the width of computer punch cards to 80 characters per line. Around 1996, the "macromolecular Crystallographic Information file" format, mmCIF, started to be phased in. An XML version of this format, called PDBML, was described in 2005. The structure files can be downloaded in any of these three formats. In fact, individual files are easily downloaded into graphics packages using web addresses:
Note: searchable structures vary over time as some become obsolete and are removed from the database.
|Number of searchable structures per year|
The significance of the structure factor files, mentioned above, is that, for PDB structures determined by X-ray diffraction that have a structure file, the electron density map may be viewed. The data of such structures is stored on the "electron density server".
These data show that most structures are determined by X-ray diffraction, but about 10% of structures are now determined by protein NMR. When using X-ray diffraction, approximations of the coordinates of the atoms of the protein are obtained, whereas estimations of the distances between pairs of atoms of the protein are found through NMR experiments. Therefore, the final conformation of the protein is obtained, in the latter case, by solving a distance geometry problem. A few proteins are determined by cryo-electron microscopy. (Clicking on the numbers in the original table will bring up examples of structures determined by that method.)
for this validation software has been made available to the public at no charge).  The data are then automatically checked for plausibility (the source code can act as deposition, data processing and distribution centers for PDB data. The data processing refers to the fact that wwPDB staff review and annotate each submitted entry.wwPDB joined in 2006. Each of the four members of  The BMRB RCSB (USA), and PDBj (Japan).