A series of PDB-related databanks for everyday needs

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ID: 300568
2014
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Abstract
We present a series of databanks (http://swift.cmbi.ru.nl/gv/facilities/) that hold information that is computationally derived from Protein Data Bank (PDB) entries and that might augment macromolecular structure studies. These derived databanks run parallel to the PDB, i.e. they have one entry per PDB entry. Several of the well-established databanks such as HSSP, PDBREPORT and PDB_REDO have been updated and/or improved. The software that creates the DSSP databank, for example, has been rewritten to better cope with π-helices. A large number of databanks have been added to aid computational structural biology; some examples are lists of residues that make crystal contacts, lists of contacting residues using a series of contact definitions or lists of residue accessibilities. PDB files are not the optimal presentation of the underlying data for many studies. We therefore made a series of databanks that hold PDB files in an easier to use or more consistent representation. The BDB databank holds X-ray PDB files with consistently represented B-factors. We also added several visualization tools to aid the users of our databanks.
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openalex_W4255594044 Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors Wouter G. Touw, Coos Baakman, Jon E. Black, Tim A. H. te Beek, Elmar Krieger, Robbie P. Joosten, Gert Vriend
Journal Nucleic Acids Research
Year 2014
DOI
10.1093/nar/gku1028
URL
https://doi.org/10.1093/nar/gku1028
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