A Searchable Database for Comparing Protein-ligand Binding Sites for the Analysis of Structure-function Relationships.
From: Institute of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.
Journal of chemical information and modeling
- Publish Date:
- ISSN: 1549-9596
- Volume: 46
- Issue: 2
- Pages: 736-42
- Medium: Print
- Language: English
- Citation (JAMA): Gold Nicola D, Jackson Richard M, et al. A Searchable Database for Comparing Protein-ligand Binding Sites for the Analysis of Structure-function Relationships.. ;46:736-42
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/.
Mesh Headings (Keywords): Binding Sites, Databases, Protein, Drug Design, Glycogen Synthase Kinase 3, Ligands, Molecular Structure, Protein Binding, Proteins, Structure-Activity Relationship
Check for Full Text / PubMed Unique Identifier (PMID): 16563004
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