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. 2002 Jan 1;30(1):379-82.
doi: 10.1093/nar/30.1.379.

MDB: the Metalloprotein Database and Browser at The Scripps Research Institute

Jesus M Castagnetto  1 , Sean W Hennessy, Victoria A Roberts, Elizabeth D Getzoff, John A Tainer, Michael E Pique
Affiliations

MDB: the Metalloprotein Database and Browser at The Scripps Research Institute

Jesus M Castagnetto et al. Nucleic Acids Res. .

Abstract

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.

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Figures

Figure 1
Figure 1
Algorithm used by the MSIT to identify and extract information about metal-binding sites in metalloproteins.
Figure 2
Figure 2
Distribution and statistics of the Zn-Nδ(His) distance (coordination number = 4, range 1.5–3.0) using the online histogram plotting tool.
See this image and copyright information in PMC

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