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

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.

Figure 1

Schematic entity-relationship model of COLUMBA. The dark gray part in the middle is the subschema that originates from the Protein Data Bank (PDB). The other subschemas are represented by a single box indicating the name of the data source and are grouped according to a broad classification of their content.

Figure 2

Screen shots of COLUMBA web-forms. (A) Interface for the full text search. (B) Query form for the metabolism information, where the result set can be restricted by information from ENZYME and KEGG.

Figure 3

Screen shots of COLUMBA query results. (A) Result set for a query requesting structures from the ENZYME class '1.-.-.-' combined with a full text condition on 'TIM barrel'. (B) COLUMBA Explorer detailed view of the PDB structure 1d3h.

Figure 4

The CATH wheel for KEGG pathways. The color of the CATH wheel represents the CATH classes, where yellow stands for alpha/beta, red for mainly alpha, blue for mainly beta, and green for Few Secondary Structures. The inner circle represents the CATH architectures (C.A.), where the width of each segment represents the number of enzymes found to exhibit that architecture. The outer circle stands for the Topology (C.A.T.). (A) shows the distribution of all enzymes participating in KEGG pathways with the '3-layer(aba) sandwich' representing the largest architecture. (B) shows the CATH wheel for the pathway 'Pyrimidine metabolism' while (C) for 'Glycolysis/Gluconeogenesis'.