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Bioinformatics Advance Access originally published online on December 5, 2006
Bioinformatics 2007 23(3):267-271; 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

In silico identification of putative metal binding motifs

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

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

*To whom correspondence should be addressed.


  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.

Contact: pgautam{at}annauniv.edu; s_anishetty{at}yahoo.co.uk

Associate Editor: Christos Ouzounis

Received on June 14, 2006; revised on November 14, 2006; accepted on November 29, 2006

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