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SuperLigands – a database of ligand structures derived from the Protein Data Bank

Elke Michalsky*, Mathias Dunkel, Andrean Goede and Robert Preissner

Author Affiliations

BCB (Berlin Center for Genome Based Bioinformatics) at Institute of Biochemistry, Charité (University Medicine Berlin), Monbijoustr. 2, 10117 Berlin, Germany

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BMC Bioinformatics 2005, 6:122  doi:10.1186/1471-2105-6-122

Published: 19 May 2005



Currently, the PDB contains approximately 29,000 protein structures comprising over 70,000 experimentally determined three-dimensional structures of over 5,000 different low molecular weight compounds. Information about these PDB ligands can be very helpful in the field of molecular modelling and prediction, particularly for the prediction of protein binding sites and function.


Here we present an Internet accessible database delivering PDB ligands in the MDL Mol file format which, in contrast to the PDB format, includes information about bond types. Structural similarity of the compounds can be detected by calculation of Tanimoto coefficients and by three-dimensional superposition. Topological similarity of PDB ligands to known drugs can be assessed via Tanimoto coefficients.


SuperLigands supplements the set of existing resources of information about small molecules bound to PDB structures. Allowing for three-dimensional comparison of the compounds as a novel feature, this database represents a valuable means of analysis and prediction in the field of biological and medical research.