The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data. Nucleic Acids Res 35:D301-D303

RCSB Protein Data Bank, Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854-8087, USA.
Nucleic Acids Research (Impact Factor: 9.11). 02/2007; 35(Database issue):D301-3. DOI: 10.1093/nar/gkl971
Source: PubMed

ABSTRACT 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.

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Available from: John L. Markley, Sep 25, 2015
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    • "These pathways typically involve transitions between different software packages and associated file formats. [A typical pathway may include: create a *.pdb file (the original file format of the worldwide Protein Databank (Berman et al., 2007) from a *.cif file with ORTEP3, software/ortep-3-for-windows or other software packages, import the *.pdb file into Meshlab, http://meshlab.sourceforge. "
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    • "The growing gap between known sequences of proteins [[1.6 9 10 8 in GenBank (Benson et al. 2008)] and 3D structures [*1 9 10 5 in PDB (Protein Data Bank; Berman et al. 2007)] is motivating the development of improved approaches to experimental structure determination. Of the two major approaches to protein structure determination, NMR spectroscopy lags behind X-ray crystallography in terms of automated approaches. "
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    • "Gene annotations are collected through ENSEMBL (Flicek et al., 2012), EMBL (Cochrane et al., 2009), GenBank (Benson et al., 2011), EntrezGene (Maglott et al., 2011), UniGene (Schuler, 1997), UniProt (Magrane and Consortium, 2011), IPI (Kersey et al., 2004), NCBI Protein (Sayers et al., 2012), RefSeq (Sayers et al., 2012), HGNC (Seal et al., 2011), GeneCards (Safran et al., 2010) and UCSC (Fujita et al., 2011) databases. Sequence domain architectures, structures and annotations are collected from PDB (Berman et al., 2007), HSSP (Schneider and Sander, 1996) and PSSH (Schafferhans et al., 2003). Functional enrichment is performed by querying the Gene Ontology repository (Ashburner et al., 2000) to collect all of the related biological processes, molecular functions and cellular components. "
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