Nucleic Acids Research Advance Access published online on October 8, 2008
Nucleic Acids Research, doi:10.1093/nar/gkn618
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Database Issue |
SuperSite: dictionary of metabolite and drug binding sites in proteins
Institute of Molecular Biology and Bioinformatics, Structural Bioinformatics Group, Charité- Medical University Berlin, Arnimallee 22, 14195 Berlin, Germany
*To whom correspondence should be addressed. Tel: +49 30 8445 1649; Fax: +49 30 8445 1551; Email: robert.preissner{at}charite.de
Received August 15, 2008. Accepted September 10, 2008.
The increasing structural information about target-bound compounds provide a rich basis to study the binding mechanisms of metabolites and drugs. SuperSite is a database, which combines the structural information with various tools for the analysis of molecular recognition. The main data is made up of 8000 metabolites including 1300 drugs, bound to about 290 000 different receptor binding sites. The analysis tools include features, like the highlighting of evolutionary conserved receptor residues, the marking of putative binding pockets and the superpositioning of different binding sites of the same ligand. User-defined compounds can be edited or uploaded and will be superimposed with the most similar co-crystallized ligand. The user can examine all results online with the molecule viewer Jmol. An implemented search algorithm allows the screening of uploaded proteins, in order to detect potential drug binding sites, which are similar to known binding pockets. The huge data set of target-bound compounds in combination with the provided analysis tools allow to inspect the characteristics of molecular recognition, especially for drug target interactions. SuperSite is publicly available at: http://bioinformatics.charite.de/supersite.
The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.