SuperLigands - a database of ligand structures derived from the Protein Data Bank.
BACKGROUND
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.


METHODS
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.


CONCLUSIONS
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.
Michalsky
Elke
E
BCB (Berlin Center for Genome Based Bioinformatics) at Institute of Biochemistry, Charité (University Medicine Berlin), Monbijoustr, 2, 10117 Berlin, Germany. elke.michalsky@charite.de
Dunkel
Mathias
M
Goede
Andrean
A
Preissner
Robert
R
D000818:Animals; D001665:Binding Sites; D019295:Computational Biology / Q000379:methods*; D003196:Computer Graphics; D003198:Computer Simulation; D003628:Database Management Systems; D016208:Databases, Factual; D030562:Databases, Protein; D006801:Humans; D020407:Internet; D008024:Ligands; D008956:Models, Chemical; D008958:Models, Molecular; D008968:Molecular Conformation; D011485:Protein Binding; D011487:Protein Conformation; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*; D016415:Sequence Alignment; D020539:Sequence Analysis, Protein; D012984:Software
D008024:Ligands; D011506:Proteins