Prediction of antimicrobial peptides toxicity based on their physico-chemical properties using machine learning techniques

Abstract

Abstract Background Antimicrobial peptides are promising tools to fight against ever-growing antibiotic resistance. However, despite many advantages, their toxicity to mammalian cells is a critical obstacle in clinical application and needs to be addressed. Results In this study, by using an up-to-date dataset, a machine learning model has been trained successfully to predict the toxicity of antimicrobial peptides. The comprehensive set of features of both physico-chemical and linguistic-based with local and global essences have undergone feature selection to identify key properties behind toxicity of antimicrobial peptides. After feature selection, the hybrid model showed the best performance with a recall of 0. 876 and a F1 score of 0. 849. Conclusions The obtained model can be useful in extracting AMPs with low toxicity from AMP libraries in clinical applications. On the other hand, several properties with local nature including positions of strand forming and hydrophobic residues in final selected features show that these properties are critical definer of peptide properties and should be considered in developing models for activity prediction of peptides. The executable code is available at https://git.io/JRZaT .

Keywords

• Antimicrobial peptides
• Peptide toxicity
• Machine learning
• Physico-chemical properties