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Oxford University Press, Nucleic Acids Research, Database(39), p. D411-D419, 2010

DOI: 10.1093/nar/gkq1105

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A series of PDB related databases for everyday needs

Journal article published in 2010 by Robbie P. Joosten, Tim A. H. te Beek, Tim Ah Te Beek, T. Beek, Elmar Krieger, Maarten L. Hekkelman ORCID, Rob Ww W. Hooft ORCID, Reinhard Schneider ORCID, Chris Sander, S. Sander, Gert Vriend
This paper is made freely available by the publisher.
This paper is made freely available by the publisher.

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Abstract

The Protein Data Bank (PDB) is the world-wide repository of macromolecular structure information. We present a series of databases that run parallel to the PDB. Each database holds one entry, if possible, for each PDB entry. DSSP holds the secondary structure of the proteins. PDBREPORT holds reports on the structure quality and lists errors. HSSP holds a multiple sequence alignment for all proteins. The PDBFINDER holds easy to parse summaries of the PDB file content, augmented with essentials from the other systems. PDB_REDO holds re-refined, and often improved, copies of all structures solved by X-ray. WHY_NOT summarizes why certain files could not be produced. All these systems are updated weekly. The data sets can be used for the analysis of properties of protein structures in areas ranging from structural genomics, to cancer biology and protein design.