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 automaticall...
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| Veröffentlicht in: | Journal of chemical information and modeling 2006-03, Vol.46 (2), p.736-742 |
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| container_title | Journal of chemical information and modeling |
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| creator | Gold, Nicola D Jackson, Richard M |
| description | 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/. |
| doi_str_mv | 10.1021/ci050359c |
| format | Article |
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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. 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Chem. Inf. Model</addtitle><date>2006-03-01</date><risdate>2006</risdate><volume>46</volume><issue>2</issue><spage>736</spage><epage>742</epage><pages>736-742</pages><issn>1549-9596</issn><eissn>1549-960X</eissn><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. 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| identifier | ISSN: 1549-9596 |
| ispartof | Journal of chemical information and modeling, 2006-03, Vol.46 (2), p.736-742 |
| issn | 1549-9596 1549-960X |
| language | eng |
| recordid | cdi_proquest_journals_216238708 |
| source | MEDLINE; ACS Publications |
| subjects | Binding Sites Comparative analysis Databases, Protein Drug Design Glycogen Synthase Kinase 3 - chemistry Glycogen Synthase Kinase 3 - metabolism Ligands Molecular Structure Protein Binding Proteins Proteins - chemistry Proteins - metabolism Structure-Activity Relationship |
| title | A Searchable Database for Comparing Protein−Ligand Binding Sites for the Analysis of Structure−Function Relationships |
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