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Practical Tools For Innovation
O'Reilly Bioinformatics Technology Conference
January 28-31, 2002 -- Tucson, AZ
Chambered Nautilus

Session

Embedding of Data and Analysis Results Using the MDB Web API

Jesus Castagnetto, Postdoctoral Research Associate, Scripps Research Institute

Track: Integration
Date: Wednesday, January 30
Time: 10:30am - 11:15am
Location: Canyon II

Since its inception in early 1998, the Metalloprotein-site Database and Browser (MDB) was designed to be a scientific resource for metalloprotein design and analysis, one that should be available to all the research community, as well as provide quantitative data for our research as part of the Metalloprotein Structure and Design Program at The Scripps Research Institute.

The MDB as a repository of geometrical information on metal-binding sites in proteins, was initially concieved to be used interactively via a web browser, not only for regular searches (e.g. list the zinc containing proteins with a resolution of up to 1.5 Angstroms) but for performing analysis of data sets (e.g. distribution of the Zn-His distances for 4-coordinate metal sites) as well. In time the need arose to allow other people, sites and even programs to access this resource non-interactively, usually to include/embed seamlessly data or analysis information from the MDB.

This talk presents the design and organization of the MDB and its web API, as well as examples on how to embed data (including an interactive structure manipulation Java applet), as well as results from analysis of geometrical information included in the MDB (e.g. metal-ligand distance distributions). Emphasis will be paid to the platform-independence of the available analysis tools being developed for the MDB, as well as the success we have had by using Open Source technologies (Apache, PHP, Python, XML and MySQL).


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