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
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).