This article is part of the supplement: Third Annual MCBIOS Conference. Bioinformatics: A Calculated Discovery

Open Access Proceedings

A Fourier Transformation based Method to Mine Peptide Space for Antimicrobial Activity

Vijayaraj Nagarajan1, Navodit Kaushik2, Beddhu Murali2, Chaoyang Zhang2, Sanyogita Lakhera3, Mohamed O Elasri1 and Youping Deng1*

Author Affiliations

1 Department of Biological Sciences, The University of Southern Mississippi, Hattiesburg, MS, 39406, USA

2 Department of Computer Science, The University of Southern Mississippi, Hattiesburg, MS, 39406, USA

3 Department of Mathematics, The University of Southern Mississippi, Hattiesburg, MS, 39406, USA

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BMC Bioinformatics 2006, 7(Suppl 2):S2  doi:10.1186/1471-2105-7-S2-S2

Published: 26 September 2006

Abstract

Background

Naturally occurring antimicrobial peptides are currently being explored as potential candidate peptide drugs. Since antimicrobial peptides are part of the innate immune system of every living organism, it is possible to discover new candidate peptides using the available genomic and proteomic data. High throughput computational techniques could also be used to virtually scan the entire peptide space for discovering out new candidate antimicrobial peptides.

Result

We have identified a unique indexing method based on biologically distinct characteristic features of known antimicrobial peptides. Analysis of the entries in the antimicrobial peptide databases, based on our indexing method, using Fourier transformation technique revealed a distinct peak in their power spectrum. We have developed a method to mine the genomic and proteomic data, for the presence of peptides with potential antimicrobial activity, by looking for this distinct peak. We also used the Euclidean metric to rank the potential antimicrobial peptides activity. We have parallelized our method so that virtually any given protein space could be data mined, in search of antimicrobial peptides.

Conclusion

The results show that the Fourier transform based method with the property based coding strategy could be used to scan the peptide space for discovering new potential antimicrobial peptides.