title: A Fourier transformation based method to mine peptide space for antimicrobial activity.
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.
  
  
  RESULTS
  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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Department of Biological Sciences, The University of Southern Mississippi, Hattiesburg, MS, 39406, USA.
authors.forename: Vijayaraj
authors.initials: V
authors.lastname: Nagarajan
authors.forename: Navodit
authors.initials: N
authors.lastname: Kaushik
authors.forename: Beddhu
authors.initials: B
authors.lastname: Murali
authors.forename: Chaoyang
authors.initials: C
authors.lastname: Zhang
authors.forename: Sanyogita
authors.initials: S
authors.lastname: Lakhera
authors.forename: Mohamed O
authors.initials: MO
authors.lastname: Elasri
authors.forename: Youping
authors.initials: Y
authors.lastname: Deng
mesh_terms: D000595:Amino Acid Sequence; D000890:Anti-Infective Agents / Q000032:analysis* / Q000737:chemistry; D019295:Computational Biology; D030562:Databases, Protein; D055808:Drug Discovery; D005583:Fourier Analysis; D008969:Molecular Sequence Data; D010455:Peptides / Q000032:analysis* / Q000737:chemistry
chemical_list: D000890:Anti-Infective Agents; D010455:Peptides