LRRML: a conformational database and an XML description of leucine-rich repeats (LRRs)
- Equal contributors
1 Department of Earth and Environmental Sciences, Ludwig-Maximilians-Universität München, Theresienstr, 41, 80333 Munich, Germany
2 Leibniz Supercomputing Centre, 85748 Garching, Germany
3 Deutsches Museum, 80538 Munich, Germany
BMC Structural Biology 2008, 8:47 doi:10.1186/1472-6807-8-47Published: 5 November 2008
Leucine-rich repeats (LRRs) are present in more than 6000 proteins. They are found in organisms ranging from viruses to eukaryotes and play an important role in protein-ligand interactions. To date, more than one hundred crystal structures of LRR containing proteins have been determined. This knowledge has increased our ability to use the crystal structures as templates to model LRR proteins with unknown structures. Since the individual three-dimensional LRR structures are not directly available from the established databases and since there are only a few detailed annotations for them, a conformational LRR database useful for homology modeling of LRR proteins is desirable.
We developed LRRML, a conformational database and an extensible markup language (XML) description of LRRs. The release 0.2 contains 1261 individual LRR structures, which were identified from 112 PDB structures and annotated manually. An XML structure was defined to exchange and store the LRRs. LRRML provides a source for homology modeling and structural analysis of LRR proteins. In order to demonstrate the capabilities of the database we modeled the mouse Toll-like receptor 3 (TLR3) by multiple templates homology modeling and compared the result with the crystal structure.