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14-September-2008 18:02:49 - Data Bank For the top secret document produced for the President of the United States, see Presidential_Daily_Briefing. for|the file format, prepared by the PDB Staff at Brookhaven National Laboratory, that describes the 3D structures of molecules found in the Protein Data Bank|Protein Data Bank file format The Protein Data Bank PDB is a repository for 3-D structural data of proteins and nucleic acids. These data, typically obtained by X-ray crystallography or NMR spectroscopy and submitted by biologists and biochemists from around the world, are released into the public domain, and can be accessed for free. See also protein structure. Contents 1 History 1.1 Growth 2 Contents 2.1 Statistics 3 File format 4 Viewing the data 5 References 5.1 Printed 6 See also 6.1 Related derived resources 6.2 Enzyme database data 6.3 Molecular graphic visualisation tools History Founded in 1971 by Drs. Edgar Meyer and Walter Hamilton Brookhaven National Laboratory, management of the Protein Data Bank was headed by Tom Koestle until 1994 and then by Joel Sussman till 1999, when it was transferred to members of the Research Collaboratory for Structural Bioinformatics RCSB. Rutgers University is the lead site and is currently under the direction of Helen M. Berman.1 The Worldwide Protein Data Bank wwPDB consists of organizations that act as deposition, data processing and distribution centers for PDB data. The founding members are RCSB PDB USA, MSD-EBI Europe and PDBj Japan. The BMRB USA group joined the wwPDB in 2006. The mission of the wwPDB is to maintain a single Protein Data Bank Archive of macromolecular structural data that is freely and publicly available to the global community. The PDB is a key resource in structural biology and is critical to more recent work in structural genomics. Countless derived databases and projects have been developed to integrate and classify the PDB in terms of protein structure, protein function and protein evolution. Growth When the PDB was originally founded it contained just 7 protein structures. Since then it has undergone an approximate exponential growth in the number of structures, which does not show any sign of falling off. The growth rate of the PDB has been the subject of fairly extensive analysis. Contents As of 24 June 2008, the database contained 51,491 released atomic coordinate entries or structures, 47,526 of that proteins, the rest being nucleic acids, nucleic acid-protein complexes, and a few other molecules. About 5,000 new structures are released each year. Data are stored in the mmCIF format specifically developed for the purpose. It is estimated that the size of the PDB archive will triple to 150,000 structures by the year 2014.2 Note that the database stores information about the exact location of all atoms in a large biomolecule although, usually without the hydrogen atoms, as their positions are more of a statistical estimate; if one is only interested in sequence data, i.e., the list of amino acids making up a particular protein or the list of nucleotides making up a particular nucleic acid, the much larger databases from Swiss-Prot and the International Nucleotide Sequence Database Collaboration should be used. Statistics As of 19 August 2008, the PDB Holdings List at RCSB reported the following statistics: Proteins Nucleic Acids Protein/NA complexes Other Total X-ray diffraction 41792 1067 1920 24 44803 NMR 6481 814 138 7 7440 Electron microscopy 132 11 49 0 192 Other 90 4 4 2 100 Total 48495 1896 2111 33 52535 Note that theoretical models are no longer accepted in the PDB. 33,017 structures in the PDB have a structure factor file. 4,054 structures in the PDB have an NMR restraint file. The current breakdown of holdings is updated weekly. File format Through the years the PDB file format has undergone many, many changes and revisions. Its original format was dictated by the width of computer punch cards. PDB Format Guide - Prepared by the PDB Staff at BNL The PDB format specification can be found here, and it is vital that you read this before looking at the raw data. Recently PDB provides a representation of PDB data in XML format, PDBML format. ftp.wwpdb.org The raw data can be downloaded from here. PDB format files can be downloaded using HTTP with URLs like this: http://www.pdb.org/pdb/files/4hhb.pdb.gz PDBML XML files can be downloaded using HTTP with URLs like this: http://www.pdb.org/pdb/files/4hhb.xml.gz ftp.ebi.ac.uk/pub/databases/rcsb/ Alternate download location for the PDB archive. www.pdb.org Statistics about the PDB can be found here. This legacy format has caused many problems with the format, and consequently there are 'clean-up' projects; The Molecular Modeling DataBase MMDB from NCBI wwPDB The MMDB uses ASN.1 and an XML conversion of this format. The wwPDB members RCSB PDB, MSD-EBI, and PDBj are working together to make the data uniform across the archive. Some believe this to be desirable; others argue that, without a universal repository of information i.e., a common dictionary, it is not possible to draw comparisons.citation needed Each structure published in PDB receives a four-character alphanumeric identifier, its PDB ID. This should not be used as an identifier for biomolecules, since often several structures for the same molecule in different environments or conformations are contained in PDB with different PDB IDs. If a biologist submits structure data for a protein or nucleic acid, wwPDB staff reviews and annotates the entry. The data are then automatically checked for plausibility. The source code for this validation software has been released for free. The main data base accepts only experimentally derived structures, and not theoretically predicted ones see protein structure prediction. Various funding agencies and scientific journals now require scientists to submit their structure data to PDB. Viewing the data The structural data can be used to visualize the biomolecules with appropriate software, such as VMD, RasMol, PyMOL, Jmol, MDL Chime, QuteMol, web browser VRML plugin or any web-based software designed to visualize and analyse the protein structures such as STING. A recent desktop software addition is Sirius. The RCSB PDB website also contains resources for education, structural genomics, and related software. References ^ Helen M. Berman - Rutgers Chemistry and Chemical Biology Department ^ PDB Archive Contains More Than 50,000 Structures. Retrieved on 2008-04-12. Printed Berman H, Henrick K, Nakamura H Dec 2003. Announcing the worldwide Protein Data Bank. Nat. Struct. Biol. 10 12: 980. doi:10.1038/nsb1203-980. PMID 14634627. Berman HM, Westbrook J, Feng Z, et al Jan 2000. The Protein Data Bank. Nucleic Acids Res. 28 1: 235-42. PMID 10592235. PMC:102472. Bernstein FC, Koetzle TF, Williams GJ, et al May 1977. The Protein Data Bank: a computer-based archival file for macromolecular structures. J. Mol. Biol. 112 3: 535-42. PMID 875032. Meyer EF Jul 1997. The first years of the Protein Data Bank. Protein Sci. 6 7: 1591-7. PMID 9232661. PMC:2143743. Sussman JL, Lin D, Jiang J, et al Nov 1998. Protein Data Bank PDB: database of three-dimensional structural information of biological macromolecules. Acta Crystallogr. D Biol. Crystallogr. 54 Pt 6 Pt 1: 1078-84. PMID 10089483. See also Crystallographic database 'Bold text'Bold textnowikiInsert non-formatted text herenowikiInsert non-formatted text here Caption1 Caption2 /nowiki/nowiki'==External links== The Worldwide Protein Data Bank wwPDB - parent site to regional hosts below RCSB Protein Data Bank - home page MSD-EBI - home page Protein Data Bank Japan - home page The PDB FAQ - frequently asked questions about the PDB and working with structural models. Related derived resources Main article: Protein structure databases Macromolecular Structure Database - MSD Home Page - project for data about macromolecular structures from the PDB. PDBWiki - PDBWiki Home Page - a website for community annotation of PDB structures. PDBsum - PDBsum Home Page - an overview of macromolecular structures in the PDB. Proteopedia - Proteopedia Home Page The collaborative, 3D encyclopedia of proteins and other molecules Enzyme database data EBI. The best mapping is provided by Kim Henrick's group at EBI as part of the MSD SIFTS initiative. PDB provide a mapping on their beta site, but it is at the whole PDB level not chain level. Search at BRENDA enzyme database portal. PDBSProtEC Molecular graphic visualisation tools PyMOL - PyMol Home Page Sirius - Sirius Home Page STING - STING Home Page RasMol - RasMol Home Page Garlic Swiss-PDB Viewer Jmol Viewer - Jmol Home Page Open Source, Java based interactive molecular viewer QuteMol - QuteMol Home Page Open Source, Win Mac, high quality interactive molecular viewer StarBiochem Java based interactive molecular viewer with integrated search of protein databank S-Animations PC based, easy to use PDB Viewer with gravity and charge simulatorca:Protein Data Bank Retrieved from http://en..org/wiki/Protein_Data_Bank Categories: Bioinformatics databases | Crystallographic databasesHidden categories: All articles with statements | Articles with statements since June 2007 Views Article Discussion this page History Personal tools Log in / create account Navigation Main page Contents Featured content Current events Random article Search Go Search Interaction Community portal Recent changes Contact Donate to Help Toolbox What links here Related changes Upload file Special pages Printable version Permanent link Cite this page Languages Dansk Deutsch Español Français í•œêµì–´ Italiano 日本語 Polski Suomi УкраїнÑ?ька ä¸æ–‡ This page was last modified on 14 September 2008, at 00:47
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