Worldwide Protein Data Bank

The Worldwide Protein Data Bank (wwPDB) is a group of organizations that act as data centers for deposition, processing and distribution for data in the Protein Data Bank. Its mission is to maintain a single Protein Data Bank archive of macromolecular structural data that is freely and publicly available to the global community. The founding members are [http://www.rcsb.org/pdb RCSB PDB (USA)] , [http://www.ebi.ac.uk/msd MSD-EBI (Europe)] and [http://www.pdbj.org PDBj (Japan)] . The [http://www.bmrb.wisc.edu/ BMRB (USA)] group joined the wwPDB in 2006.

Archive

The "Protein Data Bank archive" is the collection of flat files in the legacy PDB file format and in the mmCIF format that follows the PDB exchange dictionary (http://deposit.pdb.org/mmcif/). Each wwPDB site distributes the same files from the PDB archive.

Access

The RCSB PDB, MSD EBI, and PDBj serve as deposition, data processing and distribution sites of the PDB Archive. Each wwPDB site provides its own view of the primary data, thus providing a variety of tools and resources for the global community.

[http://www.rcsb.org/pdb] [http://www.ebi.ac.uk/msd] [http://www.pdbj.org] [http://www.bmrb.wisc.edu/]

Management

The wwPDB members agree that the RCSB will be the 'archive keeper' and will have sole write access to the PDB archive and control over the directory structure and contents. The archive keeper distributes new PDB identifiers to all deposition sites. The members of the wwPDB will undertake to use PDB 4-letter codes as set out in the agreement. The four-letter PDB identifier currently consists of a number (0-9) followed by 3 letters or numbers.

The archival PDB files will be distributed with the reserved conventional names, in the form pdbentry_id.ent, where entry_id is a PDB 4-letter code, e.g. pdb1abc.ent, for PDB format entries; rentry_idsf.ent, e.g. r1abcsf.ent, for X-ray experimental data; entry_id.mr, e.g. 1abc.mr, for NMR experimental/constraints; entry_id.cif, e.g. 1abc.cif, for mmCIF format entries; and entry_id.xml, e.g. 1abc.xml, for canonical XML format entries.

History

wwPDB formalizes the international character of the PDB and ensures that the archive will remain single and uniform. Formation of the wwPDB will be transparent to depositors. PDB depositions will continue to be accepted at all three sites and will not appear any different than it does now. Data will be equally well validated and annotated at all wwPDB sites.

By providing a formal mechanism for standardizing the presentation of PDB data, software developers and users of the data will be assured of consistent data. At the same time, it is hoped that this agreement will allow for individual creativity in how the data are presented and made available to the community.


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