TY - GEN
T1 - Designing antimicrobial peptides with weighted finite-state transducers
AU - Whelan, Christopher
AU - Roark, Brian
AU - Sönmez, Kemal
PY - 2010
Y1 - 2010
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=78650834280&partnerID=8YFLogxK
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U2 - 10.1109/IEMBS.2010.5626357
DO - 10.1109/IEMBS.2010.5626357
M3 - Conference contribution
C2 - 21095905
AN - SCOPUS:78650834280
SN - 9781424441235
T3 - 2010 Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC'10
SP - 764
EP - 767
BT - 2010 Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC'10
T2 - 2010 32nd Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC'10
Y2 - 31 August 2010 through 4 September 2010
ER -