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


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

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    • "It is well known that certain intra-residue and sequential proton-proton contacts should always be observed in NOESY spectra regardless of the structure of a protein (Wüthrich 1986). In ARECA, we have extended this analysis of NOESY contacts by reference to tables of threedimensional coordinates derived from the PACSY database (Lee et al. 2012), which includes information from both the Protein Data Bank (PDB) (Berman et al. 2007) and BioMagResBank (BMRB). The PACSY database (data retrieved in April. "

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    • "Additional human PPIs are inferred from experimental data observed in orthologous proteins. Interactome3D provides structural data for human PPIs that are derived from the Protein Data Bank (PDB) [42]. "
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    ABSTRACT: Missense mutations at protein-protein interaction (PPIs) sites, called interfaces, are important contributors to human disease. Interfaces are non-uniform surface areas characterized by two main regions, 'core' and 'rim', which differ in terms of evolutionary conservation and physico-chemical properties. Moreover, within interfaces, only a small subset of residues ('hot spots') is crucial for the binding free energy of the protein-protein complex. We performed a large-scale structural analysis of human single amino acid variations (SAVs) and demonstrated that disease-causing mutations are preferentially located within the interface core, as opposed to the rim (p< 0.01). In contrast, the interface rim is significantly enriched in polymorphisms, similar to the remaining non-interacting surface. Energetic hot spots tend to be enriched in disease-causing mutations compared to non-hot spots (p=0.05), regardless of their occurrence in core or rim residues. For individual amino acids, the frequency of substitution into a polymorphism or disease-causing mutation differed to other amino acids and was related to its structural location, as was the type of physico-chemical change introduced by the SAV. In conclusion, this study demonstrated the different distribution and properties of disease-causing SAVs and polymorphisms within different structural regions and in relation to the energetic contribution of amino acid in protein-protein interfaces, thus highlighting the importance of a structural system biology approach for predicting the effect of SAVs. Copyright © 2015. Published by Elsevier Ltd.
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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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    ABSTRACT: Ongoing software developments for creating three-dimensional (3D) printed crystallographic models seamlessly from Crystallographic Information Framework (CIF) data (*.cif files) are reported. Color versus monochrome printing is briefly discussed. Recommendations are made on the basis of our preliminary printing efforts. A brief outlook on new materials for 3D printing is given.
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