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Bioinformatics. 2012 Jun 15;28(12):1658-60. doi: 10.1093/bioinformatics/bts246. Epub 2012 May 3.

FindGeo: a tool for determining metal coordination geometry.

Author information

1
Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy. andreini@cerm.unifi.it

Abstract

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/.

PMID:
22556364
DOI:
10.1093/bioinformatics/bts246
[Indexed for MEDLINE]

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