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


METHODS
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.


CONCLUSIONS
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.
Trissl
Silke
S
Institute of Informatics, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099 Berlin, Germany. silke.trissl@informatik.hu-berlin.de
Rother
Kristian
K
Müller
Heiko
H
Steinke
Thomas
T
Koch
Ina
I
Preissner
Robert
R
Frömmel
Cornelius
C
Leser
Ulf
U
D001483:Base Sequence; D019295:Computational Biology / Q000379:methods*; D003628:Database Management Systems; D016208:Databases, Factual; D030562:Databases, Protein; D006801:Humans; D016247:Information Storage and Retrieval; D020407:Internet; D009323:Natural Language Processing; D011381:Programming Languages; D011506:Proteins / Q000737:chemistry; D040901:Proteomics; D020539:Sequence Analysis, Protein; D012984:Software; D018511:Systems Integration; D014584:User-Computer Interface
D011506:Proteins