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| - A Searchable Database for Comparing Protein−Ligand Binding Sites for the Analysis ofStructure−Function Relationships
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| - The rapid expansion of structural information for protein−ligand binding sites is potentially an importantsource 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 DataBank. This has been combined with a method for calculating binding site similarity based on geometrichashing to create a relational database for the retrieval of site similarity and binding site superposition. Itcontains an all-against-all comparison of binding sites and holds known protein−ligand binding sites, whichare made accessible to data mining. Here we demonstrate its utility in two structure-based applications: indetermining site similarity and in aiding the derivation of a receptor-based pharmacophore model. The databaseis available from http://www.bioinformatics.leeds.ac.uk/sb/.
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