- Protein structure databases
biology, a protein structure database is a databasethat is modeled around the various experimentally determined protein structures. The aim of most protein structure databases is to organize and annotate the protein structures, providing the biological community access to the experimental data in a useful way.
The Protein Data Bank
The Protein Data Bank (PDB) was established in 1971 as the central
archiveof all experimentally determined protein structure data. Today the PDB is maintained by an international consortia collectively known as the Worldwide Protein Data Bank(wwPDB). The mission of the wwPDB is to maintain a single archive of macromolecularstructural data that is freely and publicly available to the global community.
Protein structure databases
Because the PDB releases data into the
public domain, the data has been used in various other protein structure databases.
Examples of protein structure databases include (in alphabetical order);; Database of Macromolecular Movements : describes the motions that occur in proteins and other macromolecules, particularly using movies [http://www.molmovdb.org] ; JenaLib : the Jena Library of Biological Macromolecules [http://www.imb-jena.de/IMAGE.html] is aimed at a better dissemination of information on three-dimensional biopolymer structures with an emphasis on visualization and analysis.; MODBASE : a database of three-dimensional protein models calculated by comparative modeling [http://modbase.compbio.ucsf.edu] ; MSD : the Macromolecular Structure Database (MSD) the European project for the collection, management and distribution of data about macromolecular structures, derived in part from the PDB [http://www.ebi.ac.uk/msd/] ; OCA : a browser-database for protein structure/function [http://ispc.weizmann.ac.il/oca-docs/oca-home.html] - The OCA integrates information from
KEGG, OMIM, PDBselect, Pfam, PubMed, SCOP, SwissProtand others.; OPM : provides spatial positions of protein three-dimensional structures with respect to the lipid bilayer.; PDB Lite : derived from OCA, PDB Lite was provided to make it as easy as possible to find and view a macromolecule within the PDB [http://ispc.weizmann.ac.il/oca-docs/lite-why.html] ; PDBsum : provides an overview macromolecular structures in the PDB, giving schematic diagrams of the molecules in each structure and of the interactions between them [http://www.ebi.ac.uk/pdbsum/] ; PDBTM : the Protein Data Bank of Transmembrane Proteins [http://pdbtm.enzim.hu/] a selection of the PDB.; PDBWiki: a community annotated knowledge base of biological molecular structures [http://pdbwiki.org] ; Proteopedia: the collaborative, 3D encyclopedia of proteins and other molecules. A wiki that contains a page for every entry in the PDB (>50,000 pages), with a Jmolview that highlights functional sites and ligands. Offers an easy-to-use scene-authoring tool so you don't have to learn Jmol script language to create customized molecular scenes. Custom scenes are easily attached to "green links" in descriptive text that display those scenes in Jmol.; SCOP : the Structural Classification of Proteins [http://scop.mrc-lmb.cam.ac.uk/scop/] a detailed and comprehensive description of the structural and evolutionary relationships between all proteins whose structure is known. ; TOPSAN : the Open Protein Structure Annotation Network [http://www.topsan.org] a wiki designed to collect, share and distribute information about protein three-dimensional structures.
Protein structure database comparison table.
* The External Links section of the
Protein Data Bankarticle.
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