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Practical Innovation at BioCon 2003

Poster Session

The E-MSD relational database and search system

By John Tate
Dr, European Bioinformatics Institute

Structural genomics promises to deliver experimentally determined 3-D structures for many thousands of protein domains and will put each protein within a comparative modeling distance of a known protein structure. Since 1979 the Protein Data Bank (PDB) has been the central repository of macromolecular structure data, but the present flat file archive is incapable of supporting the complex tools that are required for drug discovery, molecular medicine and bioinformatics. In order to fully exploit the volume of structural data that will soon become available, new technologies must be employed. The Macromolecular Structure Database (MSD) group has developed a relational database for storing, validating and retrieving the complex structural information in the PDB. A comprehensive cleaning procedure has been carried out, to ensure data uniformity across the whole archive, and an extensive set of derived properties and goodness-of-fit indicators have been added. The MSD also includes links to many other bioinformatics databases including InterPro, GO, SwissProt, SCOP, CATH, PFAM and PROSITE. We have developed a flexible search system which exposes the power of the relational database without requiring the user to understand the complexity of the underlying schema. This search system provides a single access point for the MSD and associated databases, allowing searches on a wide range of bio-molecular properties, such as sequence, structure similarity and active site conformation. The database, and several network based-services that are built on top of it, will be available in January 2003. Our poster will describe the basic design of the database, outline some of the improvements in data quality that it provides, and will describe the services and search systems that are currently available and planned for the near future.

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