The Protein Data Bank (PDB) was founded in 1971 to provide a repository for three-dimensional (3D) structure data of experimentally determined biological macromolecules (1
). The PDB archive contains 3D coordinate data, information about the chemical content such as polymer sequence and ligand chemistry, information about the experiment used to derive the structure and some qualitative descriptions of the structure. When the PDB was in its infancy, the archive contained seven structures composed of loosely structured free text. Today, the PDB archive contains close to 40
000 structures and relies upon strict ontologies that define the content of these entries.
The data contained in the PDB are generated and submitted by scientists from around the globe to sites in the United States, Europe and Asia. The worldwide PDB (wwPDB) was established in 2003 to formally recognize the international nature of the PDB archive (2
) and to ensure that the data files remain uniform in content and format. The founding members are the RCSB PDB (USA) (1
), the Macromolecular Structure Database at the European Bioinformatics Institute (MSD-EBI) (5
) and the Protein Data Bank Japan (PDBj) at Osaka University. These wwPDB sites share responsibilities in data deposition, processing and distribution of the PDB archive, and agree to support a single, standardized archive of structural data (). The BioMagResBank (BMRB) at the University of Wisconsin-Madison (USA) (6
) became a member in 2006 and will be a deposition site for primary experimental data and PDB data.
wwPDB Data deposition and access sites
A wwPDB Advisory Committee (wwPDBAC) consists of representatives appointed by each member site as well as representatives of the international X-ray, NMR and electron microscopy (EM) communities. wwPDBAC meets yearly and provides advice about policies governing the content, format and distribution of the PDB data files.
The website (http://www.wwpdb.org/
) contains the formal agreement for the operation of the wwPDB organization, links to the deposition and access sites, and news and announcements about policies and projects related to the wwPDB.