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  • Title: A searchable database for comparing protein-ligand binding sites for the analysis of structure-function relationships.
    Author: Gold ND, Jackson RM.
    Journal: J Chem Inf Model; 2006; 46(2):736-42. PubMed ID: 16563004.
    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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