title: A series of PDB-related databanks for everyday needs.
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.
authors.affiliation: Centre for Molecular and Biomolecular Informatics, CMBI, Radboud university medical center, Geert Grooteplein Zuid 26-28 6525 GA Nijmegen, The Netherlands.
authors.forename: Wouter G
authors.initials: WG
authors.lastname: Touw
authors.affiliation: Centre for Molecular and Biomolecular Informatics, CMBI, Radboud university medical center, Geert Grooteplein Zuid 26-28 6525 GA Nijmegen, The Netherlands.
authors.forename: Coos
authors.initials: C
authors.lastname: Baakman
authors.affiliation: Centre for Molecular and Biomolecular Informatics, CMBI, Radboud university medical center, Geert Grooteplein Zuid 26-28 6525 GA Nijmegen, The Netherlands.
authors.forename: Jon
authors.initials: J
authors.lastname: Black
authors.affiliation: Bio-Prodict BV, Nieuwe Marktstraat 54E, 6511 AA Nijmegen, The Netherlands.
authors.forename: Tim A H
authors.initials: TA
authors.lastname: te Beek
authors.affiliation: Centre for Molecular and Biomolecular Informatics, CMBI, Radboud university medical center, Geert Grooteplein Zuid 26-28 6525 GA Nijmegen, The Netherlands.
authors.forename: E
authors.initials: E
authors.lastname: Krieger
authors.affiliation: Centre for Molecular and Biomolecular Informatics, CMBI, Radboud university medical center, Geert Grooteplein Zuid 26-28 6525 GA Nijmegen, The Netherlands Department of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam 1066 CX, The Netherlands.
authors.forename: Robbie P
authors.initials: RP
authors.lastname: Joosten
authors.affiliation: Centre for Molecular and Biomolecular Informatics, CMBI, Radboud university medical center, Geert Grooteplein Zuid 26-28 6525 GA Nijmegen, The Netherlands Gerrit.Vriend@radboudumc.nl.
authors.forename: Gert
authors.initials: G
authors.lastname: Vriend
mesh_terms: D019295:Computational Biology; D030562:Databases, Protein; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D012984:Software
chemical_list: D011506:Proteins