The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data

The worldwide Protein Data Bank (wwPDB) is the international collaboration that manages the deposition, processing and distribution of the PDB archive. The online PDB archive is a repository for the coordinates and related information for more than 38 000 structures, including proteins, nucleic acids and large macromolecular complexes that have been determined using X-ray crystallography, NMR and electron microscopy techniques. The founding members of the wwPDB are RCSB PDB (USA), MSD-EBI (Europe) and PDBj (Japan) [H.M. Berman, K. Henrick and H. Nakamura (2003) Nature Struct. Biol., 10, 980]. The BMRB group (USA) joined the wwPDB in 2006. The mission of the wwPDB is to maintain a single archive of macromolecular structural data that are freely and publicly available to the global community. Additionally, the wwPDB provides a variety of services to a broad community of users. The wwPDB website at provides information about services provided by the individual member organizations and about projects undertaken by the wwPDB.

[1]  Haruki Nakamura,et al.  PDBML: the representation of archival macromolecular structure data in XML , 2005, Bioinform..

[2]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..

[3]  Kengo Kinoshita,et al.  eF-site and PDBjViewer: database and viewer for protein functional sites , 2004, Bioinform..

[4]  J. Thornton,et al.  PQS: a protein quaternary structure file server. , 1998, Trends in biochemical sciences.

[5]  T. Hahn.  International tables for crystallography , 2002 .

[6]  Haruki Nakamura,et al.  Announcing the worldwide Protein Data Bank , 2003, Nature Structural Biology.

[7]  Philip E. Bourne,et al.  Macromolecular dictionary (mmCIF) , 2006 .

[8]  Roland L Dunbrack,et al.  Outcome of a workshop on archiving structural models of biological macromolecules. , 2006, Structure.

[9]  Philip E. Bourne,et al.  The RCSB PDB information portal for structural genomics , 2005, Nucleic Acids Res..

[10]  Haruki Nakamura,et al.  GASH: An improved algorithm for maximizing the number of equivalent residues between two protein structures , 2005, BMC Bioinformatics.

[11]  Sameer Velankar,et al.  E-MSD: improving data deposition and structure quality , 2005, Nucleic Acids Res..

[12]  Hiroshi Wako,et al.  ProMode: a database of normal mode analyses on protein molecules with a full-atom model , 2004, Bioinform..

[13]  G J Williams,et al.  The Protein Data Bank: a computer-based archival file for macromolecular structures. , 1977, Journal of molecular biology.

[14]  Alexandre M J J Bonvin,et al.  BioMagResBank databases DOCR and FRED containing converted and filtered sets of experimental NMR restraints and coordinates from over 500 protein PDB structures , 2005, Journal of biomolecular NMR.

[15]  Sameer Velankar,et al.  E-MSD: an integrated data resource for bioinformatics , 2004, Nucleic Acids Res..

[16]  Qing Zhang,et al.  The RCSB Protein Data Bank: a redesigned query system and relational database based on the mmCIF schema , 2004, Nucleic Acids Res..

[17]  E. Ulrich,et al.  Creation of a nuclear magnetic resonance data repository and literature database. , 1989, Protein sequences & data analysis.

[18]  Jun Zhu,et al.  BioMagResBank database with sets of experimental NMR constraints corresponding to the structures of over 1400 biomolecules deposited in the Protein Data Bank , 2003, Journal of biomolecular NMR.

[19]  Zukang Feng,et al.  The use of mmCIF architecture for PDB data management , 2006 .

[20]  G J Williams,et al.  The Protein Data Bank: a computer-based archival file for macromolecular structures. , 1978, Archives of biochemistry and biophysics.