Designing antimicrobial peptides with weighted finite-state transducers

Christopher Whelan, Brian Roark, Mustafa (Kemal) Sonmez

Research output: Chapter in Book/Report/Conference proceedingConference contribution

4 Citations (Scopus)

Abstract

The design of novel antimicrobial peptides (AMPs) is an important problem given the rise of drug-resistant bacteria. However, the large size of the sequence search space, combined with the time required to experimentally test or simulate AMPs at the molecular level makes computational approaches based on sequence analysis attractive. We propose a method for designing novel AMPs based on learning from n-gram counts of classes of amino acid residues, and then using weighted finite-state machines to produce sequences that incorporate those features that are strongly associated with AMP sequences. Finite-state machines are able to generate sequences that include desired n-gram features. We use this approach to generate candidate novel AMPs, which we test using third-party prediction servers. We demonstrate that our framework is capable of producing large numbers of novel peptide sequences that share features with known antimicrobial peptides.

Original languageEnglish (US)
Title of host publication2010 Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC'10
Pages764-767
Number of pages4
DOIs
StatePublished - 2010
Event2010 32nd Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC'10 - Buenos Aires, Argentina
Duration: Aug 31 2010Sep 4 2010

Other

Other2010 32nd Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC'10
CountryArgentina
CityBuenos Aires
Period8/31/109/4/10

Fingerprint

Peptides
Transducers
Finite automata
Amino acids
Bacteria
Servers

ASJC Scopus subject areas

  • Biomedical Engineering

Cite this

Whelan, C., Roark, B., & Sonmez, M. K. (2010). Designing antimicrobial peptides with weighted finite-state transducers. In 2010 Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC'10 (pp. 764-767). [5626357] https://doi.org/10.1109/IEMBS.2010.5626357

Designing antimicrobial peptides with weighted finite-state transducers. / Whelan, Christopher; Roark, Brian; Sonmez, Mustafa (Kemal).

2010 Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC'10. 2010. p. 764-767 5626357.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Whelan, C, Roark, B & Sonmez, MK 2010, Designing antimicrobial peptides with weighted finite-state transducers. in 2010 Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC'10., 5626357, pp. 764-767, 2010 32nd Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC'10, Buenos Aires, Argentina, 8/31/10. https://doi.org/10.1109/IEMBS.2010.5626357
Whelan C, Roark B, Sonmez MK. Designing antimicrobial peptides with weighted finite-state transducers. In 2010 Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC'10. 2010. p. 764-767. 5626357 https://doi.org/10.1109/IEMBS.2010.5626357
Whelan, Christopher ; Roark, Brian ; Sonmez, Mustafa (Kemal). / Designing antimicrobial peptides with weighted finite-state transducers. 2010 Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC'10. 2010. pp. 764-767
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