FindGeo: a tool for determining metal coordination geometry

Bioinformatics
Claudia AndreiniSerena Lorenzini

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. FindGeo is freely available as a web service and as a stand-alone program at http://metalweb.cerm.unifi.it/tools/findgeo/.

References

Dec 11, 1999·Nucleic Acids Research·H M BermanP E Bourne
Nov 7, 1996·Chemical Reviews·Richard H. HolmEdward I. Solomon
May 31, 2002·Acta Crystallographica. Section B, Structural Science·Frank H Allen
Nov 18, 2005·The Journal of Biological Chemistry·Lucia BanciElena Gaggelli
Jul 28, 2007·Proteins·Mariana BaborMarvin Edelman
Nov 1, 2007·Australian Dental Journal·L G Do, K F Roberts-Thomson
Mar 7, 2009·Journal of Molecular Biology·Claudia AndreiniJanet M Thornton
Aug 14, 2009·Nature·Kevin J WaldronNigel J Robinson
Aug 14, 2009·Nature·Yi LuNicholas M Marshall
Nov 13, 2010·Metallomics : Integrated Biometal Science·Jens Müller
Nov 2, 2011·PloS One·Claudia AndreiniGabriele Cavallaro
Nov 19, 2011·Nucleic Acids Research·Joachim SchnablRoland K O Sigel

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Citations

Nov 17, 2012·Nucleic Acids Research·Claudia AndreiniAntonio Rosato
Oct 6, 2015·PloS One·Priyabrata PanigrahiC G Suresh
Aug 20, 2016·Biochemistry·John J TannerMichael T Henzl
Oct 28, 2017·Nucleic Acids Research·Valeria PutignanoClaudia Andreini
Oct 20, 2018·Dalton Transactions : an International Journal of Inorganic Chemistry·Konstantina PringouriJeremy M Rawson
Apr 17, 2020·Nucleic Acids Research·Katrin Schöning-StierandMatthias Rarey
Feb 9, 2017·Bioscience Reports·Gunseli Bayram Akcapinar, Osman Ugur Sezerman
Jun 20, 2020·Dalton Transactions : an International Journal of Inorganic Chemistry·Natalija Pantalon JurajSrećko I Kirin
Apr 9, 2021·Protein Science : a Publication of the Protein Society·Hoang Nguyen, Jesse Kleingardner
Jun 3, 2021·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Dóra Lakk-BogáthJózsef Kaizer
Jun 19, 2021·Nature Communications·Ryan FeehanJoanna S G Slusky
Aug 6, 2021·Acta Crystallographica. Section C, Structural Chemistry·Seik Weng Ng
Nov 28, 2019·Inorganic Chemistry·Natalija Pantalon JurajSrećko I Kirin

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