A searchable database for comparing protein-ligand binding sites for the analysis of structure-function relationships |
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Authors: | Gold Nicola D Jackson Richard M |
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Institution: | Institute of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK. |
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Abstract: | 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/. |
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