Worldwide Protein Data Bank

Berman, H.M., K. Henrick, and H. Nakamura. 2003. Announcing the worldwide Protein Data Bank. Nat. Struct. Biol. 10 980. 

Berman H, Henrick K, Nakamura H, Markley JL. The worldwide Protein Data Bank (wwPDB) ensuring a single, uniform archive of PDB data. Nucleic Acids Res. 2007 35 D301-D303. 

Worldwide Protein Data Bank http //www.wwpdb.org... 

The Cambridge Structural Database, ChemSpider and the Worldwide Protein Data Bank are three widely used online resources that contain structural information. 

The Worldwide Protein Data Bank (www.wwPDB.org) consists of a number of organisations that act as deposition, data processing and distribution centres for the PDB data. Its mission is to maintain a single PDB archive of macromolecular structural data that is freely and publicly available to the global community. 

Berman, H. M., Olson, W. K., Beveridge, D. 1., Westbrook, J., Gelbin A., Demeny T., Hsieh S.-H., Srinivasan, A. R., Schneider, B. (1992). The nucleic acid database. A comprehensive relational database of three-dimensional structures of nucleic acids. Biophysical Journal, 63, 751. Berman, H. M., Henrick, K., Nakamura, H. (2003). Announcing the worldwide protein data bank. Nature Structural Molecular Biology, 10, 980. Bernal, J. D., Fowler, R. H. (1933). A theory of water and ionic solution, with particular reference to hydrogen and hydroxyl ions. Journal of Chemical Physics, 1, 515. 

H. Berman, K. Henrick, H. Nakamura, and J. L. Markley, Nucleic Acids Res., 35, D301-D303 (2007). The Worldwide Protein Data Bank (wwPDB) Ensuring a Single, Uniform Archive of PDB Data. 

Protein Data Bank (Section 27 20) A central repository in which crystallographic coordinates for biological mole cules especially proteins are stored The data are accessi ble via the Worldwide Web and can be transformed into three dimensional images with appropriate molecular modeling software... 

Molecular databases and the associated data banks require the development of a conceptual structure for the information stored about the molecules, descriptive language representing the data, and methods for analysis enabling molecular modeling, similarity searches, classification, visualization, or other uses of the database.320 Currendy, the Protein Data Bank (PDB http 7www.rcsb.org/pdb/) is one of the best known examples of a molecular database. The PDB is a worldwide archive of three-dimensional structural data of biological macromolecules.321 The PDB is a common accentor to many structural databases.322 The success of... 

In case of proteins, one of the most decisive facts was also the availability of the Protein Data Bank, a result of many-year extensive work of X-ray and NMR worldwide communities. Only thanks to the Protein Data Bank, it was possible to acquire gradually the necessary knowledge about what are and what decides the secondary structures, and to create the statistical potentials useful in such procedure as REFINER. The statistical potentials were able to compensate for our current lack of physical/chemical understanding of many-body interactions. Without a similar data base (in other domains of chemistry), it is difficult to imagine a proper calibration of theoretical tools. 

The Protein Data Bank (PDB http //www.pdb.org) is the worldwide repository of three-dimensional structural data of biological macromolecules, such as proteins and nucleic acids (Berman et al. 2003). The Protein Data Bank uses several text file-based formats for data deposition, processing, and archiving. The oldest of these is the Protein Data Bank format (Bernstein 1977), which is used both for deposition and for retrieval of results. It is a plain-text format whose main part, a so-called primary structure section, contains the atomic coordinates within the sequence of residues (e.g., nucleotides or amino acids) in each chain of the macromolecule. Embedded in these records are chain identifiers and sequence numbers that allow other records to reference parts of the sequence. Apart from structural data, the PDB format also allows for storing of various metadata such as bibliographic data, experimental conditions, additional stereochemistry information, and so on. However, the amount of metadata types available is rather limited owing to the age of the PDB format and to its relatively strict syntax rules. 

CML is the best known of the XML notations for capture of structural data, but several other formats use XML-based syntax. The Protein Data Bank (PDB) (http // www.wwpdb.org/) is the single worldwide repository for macromolecular structure data. A representation of the Brookhaven PDB is available in an XML format called PDBML (Westbrook et al. 2005). PDBML provides a way to export structures and information about them from a relational database. Another database that offers... 

Perhaps the most useful of all biological databases is the Protein Data Bank (PDB), operated by the Research Collaboratory for Structural Bioinformatics (RCSB). The PDB is a worldwide repository of X-ray and N.VIR structural data for biological macromolecules. In early 2007, data for more than 40,000 structures were available, and more than 6000 new structures were being added yearly. To access the Protein Data Bank, go to http //w W W,rcsb.org/pdb/ and a home page like that shown in Figure 26.11 will appear. As wdth much that is available online, however, the PDB site is changing rapidly, so you may not see quite the same thing. 

At Brookhaven National Laboratory, New York, the Protein Data Bank (PDB) was established in 1971, and has become a repository for protein coordinates which are shared between scientists worldwide. The PDB is a very important tool and the basis for rational, stracture-based drug design -a prerequisite for the development of modern biopharmaceuticals. 

Research progress in bioinorganic chemistry has been greatly assisted in recent years by the development of methods to solve protein structures using X-ray diffraction and NMR spectroscopy. Readers are encouraged to make use of the Protein Data Bank (PDB) to update the information given in this chapter information is available using the worldwide web (http //www/rcsb.org/pdb). ... 

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