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Open Access Database

Columba: an integrated database of proteins, structures, and annotations

Silke Trißl1, Kristian Rother2*, Heiko Müller1, Thomas Steinke3, Ina Koch4, Robert Preissner2, Cornelius Frömmel2 and Ulf Leser1

Author Affiliations

1 Institute of Informatics, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099 Berlin, Germany

2 Institute of Biochemistry, Charité Universitätsmedizin Berlin, Monbijoustraß e 2a, 10117 Berlin, Germany

3 Zuse Institute Berlin, Takustrasse 7, 14195 Berlin, Germany

4 Technische Fachhochschule Berlin, Seestr. 64, 13347 Berlin, Germany

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BMC Bioinformatics 2005, 6:81  doi:10.1186/1471-2105-6-81

Published: 31 March 2005

Abstract

Background

Structural and functional research often requires the computation of sets of protein structures based on certain properties of the proteins, such as sequence features, fold classification, or functional annotation. Compiling such sets using current web resources is tedious because the necessary data are spread over many different databases. To facilitate this task, we have created COLUMBA, an integrated database of annotations of protein structures.

Description

COLUMBA currently integrates twelve different databases, including PDB, KEGG, Swiss-Prot, CATH, SCOP, the Gene Ontology, and ENZYME. The database can be searched using either keyword search or data source-specific web forms. Users can thus quickly select and download PDB entries that, for instance, participate in a particular pathway, are classified as containing a certain CATH architecture, are annotated as having a certain molecular function in the Gene Ontology, and whose structures have a resolution under a defined threshold. The results of queries are provided in both machine-readable extensible markup language and human-readable format. The structures themselves can be viewed interactively on the web.

Conclusion

The COLUMBA database facilitates the creation of protein structure data sets for many structure-based studies. It allows to combine queries on a number of structure-related databases not covered by other projects at present. Thus, information on both many and few protein structures can be used efficiently. The web interface for COLUMBA is available at http://www.columba-db.de webcite.