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Bioinformatics Advance Access published online on December 5, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl617
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© The Author (2006). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received June 14, 2006
Revised November 14, 2006
Accepted November 29, 2006

Discovery note

In silico identification of putative metal binding motifs

Richard Thilakaraj 1, Krishnan Raghunathan 1, Sharmila Anishetty 1, and Gautam Pennathur 1 *

1 Centre for Biotechnology, Anna University, Chennai 600 025, India

* To whom correspondence should be addressed.
Gautam Pennathur, E-mail: pgautam{at}annauniv.edu


  Abstract

Metal ion binding domains are found in proteins that mediate transport, buffering or detoxification of metal ions. In this study, we have performed an in silico analysis of metal binding proteins and have identified putative metal binding motifs for the ions of cadmium, cobalt, zinc, arsenic, mercury, magnesium, manganese, molybdenum and nickel. A pattern search against the UniProtKB/Swiss-Prot and UniProtKB/TrEMBL databases yielded true positives in each case showing the high specificity of the motifs. Motifs were also validated against PDB structures and site directed mutagenesis studies.

Associate Editor: Christos Ouzounis
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