The Metalloprotein Database and Browser (MDB, http://metallo.scripps.edu) 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 develoments :
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 (http://www.sdsc.edu/CCMS), 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.