dsAMP and dsAMPGAN: Deep Learning Networks for Antimicrobial Peptides Recognition and Generation.

Abstract

Antibiotic resistance is a growing public health challenge. Antimicrobial peptides (AMPs) effectively target microorganisms through non-specific mechanisms, limiting their ability to develop resistance. Therefore, the prediction and design of new AMPs is crucial. Recently, deep learning has spurred interest in computational approaches to peptide drug discovery. This study presents a novel deep learning framework for AMP classification, function prediction, and generation. We developed discoverAMP (dsAMP), a robust AMP predictor using CNN Attention BiLSTM and transfer learning, which outperforms existing classifiers. In addition, dsAMPGAN, a Generative Adversarial Network (GAN)-based model, generates new AMP candidates. Our results demonstrate the superior performance of dsAMP in terms of sensitivity, specificity, Matthew correlation coefficient, accuracy, precision, F1 score, and area under the ROC curve, achieving >95% classification accuracy with transfer learning on a small dataset. Furthermore, dsAMPGAN successfully synthesizes AMPs similar to natural ones, as confirmed by comparisons of physical and chemical properties. This model serves as a reliable tool for the identification of novel AMPs in clinical settings and supports the development of AMPs to effectively combat antibiotic resistance.