Determine the coordination geometry of metals in biological macromolecules

FindGeo

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

Further information