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  1. Columba
    Resource Category : Databases -> Structure Databases -> Protein structure

    Brief Description : Columba is a database that integrates twelve annotation sources on protein structures in one data warehouse. The database contains records for all structures from the PDB, annotation on folding classification from SCOP and CATH, metabolic pathways from KEGG and the Boehringer map, the ENZYME database, DSSP secondary structures, non-redundant lists from PISCES and the PDB itself and references to scientific publications parsed from PDB and taken from Swiss-Prot. Using the links from the PDBSprotEC database, chainwise references to Swiss-Prot entries are also contained, allowing to annotate the structures by the NCBI taxonomy and the Gene Ontology Terms. The Columba web interface allows to set restrictions on each of the data sources mentioned above. By defining several filter conditions on different data sources, the desired data set can be extracted from the complete PDB. This way, Columba can answer questions such as - Which protein chains have a TIM-barrel fold? - Which proteins in the citric acid cycle have a resolved structure? - Which protein chains have a helix-turn-helix motif matching a given regular expression? In addition to compiling data sets summary pages for each individual structure can be browsed.

    Institute/s :
    Institute of Informatics, Humboldt-Universitat zu Berlin, Unter den Linden 6, 10099 Berlin, Germany
    Address of Institute/s :
    Institute of Informatics, Humboldt-Universitat zu Berlin, Unter den Linden 6, 10099 Berlin, Germany
    Country : Germany

    Associated Institutes :

    • Institute of Informatics, Humboldt-Universitat zu Berlin, Unter den Linden 6, 10099 Berlin, Germany
    • Institute of Biochemistry, Charite Universitatsmedizin Berlin, Monbijoustrabe 2a, 10117 Berlin, Germany
    • Zuse Institute Berlin, Takustrasse 7, 14195 Berlin, Germany
    • Technische Fachhochschule Berlin, Seestr. 64, 13347 Berlin, Germany

    Associated Country : Germany


    Authors/Contributors : Silke Tribl; Kristian Rother; Heiko Muller; Thomas Steinke; Ina Koch; Robert Preissner; Cornelius Frommel; Ulf Leser
    Contact Email : kristian.rother@charite.de
    Year : 2005
    Language : English