Machine learning-enabled predictive modeling to precisely identify the antimicrobial peptides

The ubiquitous antimicrobial peptides (AMPs), with a broad range of antimicrobial activities, represent a great promise for combating the multi-drug resistant infections. In this study, using a large and diverse set of AMPs (2638) and non-AMPs (3700), we have explored a variety of machine learning classifiers to build in silico models for AMP prediction, including Random Forest (RF), k-Nearest Neighbors (k-NN), Support Vector Machine (SVM), Decision Tree (DT), Naive Bayes (NB), Quadratic Discriminant Analysis (QDA), and ensemble learning. Among the various models generated, the RF classifier-based model top-performed in both the internal [Accuracy: 91.40%, Precision: 89.37%, Sensitivity: 90.05%, and Specificity: 92.36%] and external validations [Accuracy: 89.43%, Precision: 88.92%, Sensitivity: 85.21%, and Specificity: 92.43%]. In addition, the RF classifier-based model correctly predicted the known AMPs and non-AMPs; those kept aside as an additional external validation set. The performance assessment revealed three features viz. ChargeD2001, PAAC12 (pseudo amino acid composition), and polarity T13 that are likely to play vital roles in the antimicrobial activity of AMPs. The developed RF-based classification model may further be useful in the design and prediction of the novel potential AMPs.