Characterization and identification of natural antimicrobial peptides on different organisms

Chia Ru Chung, Jhih Hua Jhong, Zhuo Wang, Siyu Chen, Yu Wan, Jorng Tzong Horng, Tzong Yi Lee

Research output: Contribution to journalArticlepeer-review

12 Scopus citations

Abstract

Because of the rapid development of multidrug resistance, conventional antibiotics cannot kill pathogenic bacteria efficiently. New antibiotic treatments such as antimicrobial peptides (AMPs) can provide a possible solution to the antibiotic-resistance crisis. However, the identification of AMPs using experimental methods is expensive and time-consuming. Meanwhile, few studies use amino acid compositions (AACs) and physicochemical properties with different sequence lengths against different organisms to predict AMPs. Therefore, the major purpose of this study is to identify AMPs on seven categories of organisms, including amphibians, humans, fish, insects, plants, bacteria, and mammals. According to the one-rule attribute evaluation, the selected features were used to construct the predictive models based on the random forest algorithm. Compared to the accuracies of iAMP-2L (a web-server for identifying AMPs and their functional types), ADAM (a database of AMP), and MLAMP (a multi-label AMP classifier), the proposed method yielded higher than 92% in predicting AMPs on each category. Additionally, the sensitivities of the proposed models in the prediction of AMPs of seven organisms were higher than that of all other tools. Furthermore, several physicochemical properties (charge, hydrophobicity, polarity, polarizability, secondary structure, normalized van der Waals volume, and solvent accessibility) of AMPs were investigated according to their sequence lengths. As a result, the proposed method is a practical means to complement the existing tools in the characterization and identification of AMPs in different organisms.

Original languageEnglish
Article number986
JournalInternational Journal of Molecular Sciences
Volume21
Issue number3
DOIs
StatePublished - Feb 2020

Keywords

  • Antimicrobial peptides
  • Feature selection
  • Machine learning
  • Organisms
  • Sequence analysis

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