Metals are essential for the structure and function of many proteins and nucleic acids. The geometric arrangement of the atoms that coordinate a metal in a biological macromolecule is an important determinant of the specificity and role of that metal. FindGeo quickly finds and determines the coordination geometry of selected, or all, metals in a given structure. It works by superimposing the metal-coordinating atoms in the input structure (a PDB file either on a local disk or downloaded from the PDB) to a library of templates with alternative ideal geometries, which are ranked by RMSD to identify the best geometry assignment.
FindGeo supports scientists by:
- minimizing errors in the assignment of geometries
- promoting a uniform terminology and classification of geometries and
- providing a reliable basis for structure–function relationship studies where coordination geometry is a relevant parameter.
Possible large scale applications of FindGeo - for which the stand-alone program will be most suitable - include:
- analysis of all metal sites in PDB structures or in nucleic acid databases
- structure–function studies of correlations between coordination geometry and other parameters (e.g. metal function, oxidation state)
- protein function prediction in conjunction with predictors of metal sites
FindGeo is freely available as a web service and as a stand-alone program