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.
Highlights
We present a series of databases that run parallel to the Protein Data Bank (PDB)
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
The Protein Data Bank (PDB) [1,2,3,4] is the world-wide repository of macromolecular structures solved by X-ray diffraction, NMR, orelectron microscopy
Summary
The Protein Data Bank (PDB) [1,2,3,4] is the world-wide repository of macromolecular structures solved by X-ray diffraction, NMR, or (cryo-)electron microscopy. Secondary structure of proteins http://swift.cmbi.ru.nl/gv/dssp/ Multiple sequence alignments of UniProtKB against PDB files http://swift.cmbi.ru.nl/gv/hssp/ Reports about errors and anomalies in macromolecules http://swift.cmbi.ru.nl/gv/pdbreport/ Re-refined PDB files solved by X-ray crystallography http://www.cmbi.ru.nl/pdb_redo/ Searchable summaries of PDB file information ftp://ftp.cmbi.ru.nl/pub/molbio/data/pdbfinder/ As PDBFINDER, but with much extra information added ftp://ftp.cmbi.ru.nl/pub/molbio/data/pdbfinder2/ Quality-sorted culled lists of protein chains in the PDB http://swift.cmbi.ru.nl/gv/select/ Explanation why entries in other databases cannot exist http://www.cmbi.ru.nl/WHY_NOT/
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