MetalPDB: a database of metal sites in biological macromolecular structures.

We present here MetalPDB (freely accessible at http://metalweb.cerm.unifi.it), a novel resource aimed at conveying the information available on the three-dimensional (3D) structures of metal-binding biological macromolecules in a consistent and effective manner. This is achieved through the systematic and automated representation of metal-binding sites in proteins and nucleic acids by way of Minimal Functional Sites (MFSs). MFSs are 3D templates that describe the local environment around the metal(s) independently of the larger context of the macromolecular structure embedding the site(s), and are the central objects of MetalPDB design. MFSs are grouped into equistructural (broadly defined as sites found in corresponding positions in similar structures) and equivalent sites (equistructural sites that contain the same metals), allowing users to easily analyse similarities and variations in metal-macromolecule interactions, and to link them to functional information. The web interface of MetalPDB allows access to a comprehensive overview of metal-containing biological structures, providing a basis to investigate the basic principles governing the properties of these systems. MetalPDB is updated monthly in an automated manner.

FindGeo: a tool for determining metal coordination geometry.

UNLABELLED: Metals are essential for the structure and function of many proteins and nucleic acids. The geometrical arrangement of the atoms that coordinate a metal in a biological macromolecule is an important determinant of the specificity and role of that metal. At present, however, this information can be retrieved only from the literature, which sometimes contains an improper or incorrect description of the geometry, and often lacks it altogether. Thus, we developed FindGeo to quickly and easily determine the coordination geometry of selected, or all, metals in a given structure. FindGeo works by superimposing the metal-coordinating atoms in the input structure to a library of templates with alternative ideal geometries, which are ranked by RMSD to identify the best geometry assignment. AVAILABILITY: FindGeo is freely available as a web service and as a stand-alone program at http://metalweb.cerm.unifi.it/tools/findgeo/.