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Metalloprotein Site Database

NAR Molecular Biology Database Collection entry number 179
Castagnetto, J.M., Hennessy, S.W., Roberts, V.A., Getzoff, E.D., Tainer, J.A., Pique, M.E.
The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037

Database Description

The Metalloprotein Database and Browser (MDB, at The Scripps Research Institute is a web-accessible resource for metalloprotein research. It offers the scientific community quantitative information on geometrical parameters of metal-binding sites in protein structures available from the Protein Data Bank (PDB). The MDB also offers analytical tools for the examination of trends or patterns in the indexed metal-binding sites. A user can perform interactive searches, metal-site structure visualization (via a Java applet), and analysis of the quantitative data by accessing the MDB through a web browser without requiring an external application or platform-dependent plugin. The MDB also has a non-interactive interface with which other web sites and network-aware applications can seamlessly incorporate data or statistical analysis results from metal-binding sites. The information contained in the MDB is periodically updated with automated algorithms that find and index metal sites from new protein structures released by the PDB.

Recent Developments

Interactive tools for statistical analysis of metal-binding site geometries and trends. Indexing of second-shell binding data. Implementation of multi-protocol web services (REST, XML-RPC, and SOAP) to allow other resources to interact with the MDB.


The MDB is part of the Metalloprotein Structure and Design Program Project at TSRI, funded by NIH grant P01-GM48495. The macromolecular Java viewer was developed as part of the Computational Center for Macromolecular Structure (, funded by NSF grant BIO/DBI 99-04559.


Castagnetto, J.M.; Hennessy, S.W.; Roberts, V.A.; Getzoff, E.D.; Tainer, J.A.; Pique, M.E. 'MDB: the Metalloprotein Database and Browser at The Scripps Research Institute'. Nucleic Acids Res. 2002, 30(1): 379-382.

Go to the abstract in the NAR 2002 Database Issue.
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