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. 2015 Jan;43(Database issue):D364-8.
doi: 10.1093/nar/gku1028. Epub 2014 Oct 28.

A series of PDB-related databanks for everyday needs

Wouter G Touw  1 , Coos Baakman  1 , Jon Black  1 , Tim A H te Beek  2 , E Krieger  1 , Robbie P Joosten  3 , Gert Vriend  4
Affiliations

A series of PDB-related databanks for everyday needs

Wouter G Touw et al. Nucleic Acids Res. 2015 Jan.

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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Figures

Figure 1.
Figure 1.
Schematic illustration of the absence of symmetry related waters, ions and ligands. Three crystal cells are shown. These three cells, obviously, contain the same molecules. The brown ellipses A and B are two macromolecules, and the small blue circle is a small molecule, e.g. water, that sits packed between two copies of macromolecule A. Each macromolecule A thus has a contact with two small blue circles. The PDB file corresponding to this example will only contain the content of one cell. So when the PDB file is inspected visually, only one of the blue circles will be seen.
Figure 2.
Figure 2.
VASE screenshot. A selected position in the HSSP alignment (red column in the top panel) is shown in the structure (bottom right) and in the calculated entropy and variability table (bottom left). The inset shows an entropy-variability plot.
See this image and copyright information in PMC

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