A searchable database for comparing protein-ligand binding sites for the analysis of structure-function relationships.
The rapid expansion of structural information for protein-ligand binding sites is potentially an important source of information in structure-based drug design and in understanding ligand cross reactivity and toxicity. We have developed a large database of ligand binding sites extracted automatically from the Protein Data Bank. This has been combined with a method for calculating binding site similarity based on geometric hashing to create a relational database for the retrieval of site similarity and binding site superposition. It contains an all-against-all comparison of binding sites and holds known protein-ligand binding sites, which are made accessible to data mining. Here we demonstrate its utility in two structure-based applications: in determining site similarity and in aiding the derivation of a receptor-based pharmacophore model. The database is available from http://www.bioinformatics.leeds.ac.uk/sb/.
Gold
Nicola D
ND
Institute of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.
Jackson
Richard M
RM
D001665:Binding Sites; D030562:Databases, Protein; D015195:Drug Design; D038362:Glycogen Synthase Kinase 3 / Q000737:chemistry / Q000378:metabolism; D008024:Ligands; D015394:Molecular Structure; D011485:Protein Binding; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism; D013329:Structure-Activity Relationship
D008024:Ligands; D011506:Proteins; D038362:Glycogen Synthase Kinase 3