Worldwide Protein Data Bank
Encyclopedia
The Worldwide Protein Data Bank, wwPDB, is an organization whose mission, according to its website, is "to maintain a single Protein Data Bank
Archive of macromolecular structural data that is freely and publicly available to the global community." Given the open access goal, it is somewhat ironic that the announcement of the collaborative was made in a pay-for-access journal
(Nature Structual Biology).
The organization has four members:
The wwPDB was founded in 2003 by RCSB PDB (USA), PDBe (Europe) and PDBj (Japan). In 2006 BMRB (USA) joined the wwPDB.
Each member's site can accept structural data and process the data. The processed data is sent to the "archive keeper", which is agreed to be RCSB PDB. This ensures that there is only one version of the data which is identical for all users. The modified database is then made available to the other wwPDB members, each of whom makes the resulting structure files available through their websites to the public. (Data is accessed from the wwPDB website itself only through links to the member websites.) The member sites are more than just mirrors of the archive keeper, because the members offer different tools on their websites for analysing the structures in the database.
Accomplishments (taken from wwPDB annual reports)
Protein Data Bank
The Protein Data Bank is a repository for the 3-D structural data of large biological molecules, such as proteins and nucleic acids....
Archive of macromolecular structural data that is freely and publicly available to the global community." Given the open access goal, it is somewhat ironic that the announcement of the collaborative was made in a pay-for-access journal
Scientific journal
In academic publishing, a scientific journal is a periodical publication intended to further the progress of science, usually by reporting new research. There are thousands of scientific journals in publication, and many more have been published at various points in the past...
(Nature Structual Biology).
The organization has four members:
- Research Collaboratory for Structural Bioinformatics Protein Database, RCSB PDB (USA)
- Protein Data Bank in Europe, PDBe
- Protein Data Bank Japan, PDBj
- Biological Magnetic Resonance Data Bank, BMRB (USA)
The wwPDB was founded in 2003 by RCSB PDB (USA), PDBe (Europe) and PDBj (Japan). In 2006 BMRB (USA) joined the wwPDB.
Each member's site can accept structural data and process the data. The processed data is sent to the "archive keeper", which is agreed to be RCSB PDB. This ensures that there is only one version of the data which is identical for all users. The modified database is then made available to the other wwPDB members, each of whom makes the resulting structure files available through their websites to the public. (Data is accessed from the wwPDB website itself only through links to the member websites.) The member sites are more than just mirrors of the archive keeper, because the members offer different tools on their websites for analysing the structures in the database.
Accomplishments (taken from wwPDB annual reports)
- 2008 The wwPDB now requires that, in addition to atomic coordinates, structure factor amplitudes and intensities (for crystal structure depositions) and NMR restraints (for NMR structure depositions) must be deposited as a prerequisite for receiving a PDB ID.
- 2007 Rolled out a remediated PDB. Remediation included changing the nomenclature to conform to IUPAC standards.