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Columba (discontinued)


NAR Molecular Biology Database Collection entry number 883
Rother K.1, Triß S.2, MÜueller H.2, Preißner R.1, Steinke T.3, Leser U.2, FrÖmmel C.1
1Protein Structure Theory Group, Institute of Biochemistry at the Charite, Charite-UniversitÄt zu Berlin, Monbijoustrasse 2, 10117 Berlin, Germany
2Knowledge Management in Bioinformatics, Institute of Informatics, Humboldt-UniversitÄt zu Berlin, Rudower Chaussee 25, 12489 Berlin, Germany
3Computer Science Research Dept., Konrad-Zuse-Zentrum f. Informationstechnik Berlin (ZIB), Takustrasse 7, 14195 Berlin, Germany

Database 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.

Recent Developments

Recently, the result pages of Columba have been made available in XML format besides HTML output. Also, the 3D-viewer JMol was included into the website to visualize PDB structures, chains and SCOP domains on the web. The summary page for a particular PDB entry is available via the URL http://elfie.bcbio.de/columba/columba.cgi?action=single_result&pdbid=1cse .

Acknowledgements

This research was supported by the German Ministry of Education and Research (BMBF), grant no. 0312705B.

References

1. Columba: an integrated database of proteins, structures, and annotations (2005) Trißl S, Rother K, MÜller H, Steinke T, Koch I, Preissner R, FrÖmmel C, Leser U. BMC Bioinformatics, 6:81

Subcategory: Protein structure

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