PepNet: an interpretable neural network for anti-inflammatory and antimicrobial peptides prediction using a pre-trained protein language model
Year: 2024
Type: article
Abstract: Identifying anti-inflammatory peptides (AIPs) and antimicrobial peptides (AMPs) is crucial for the discovery of innovative and effective peptide-based therapies targeting inflammation and microbial infections. However, accurate identification of AIPs and AMPs remains a computational challenge mainly due to limited utilization of peptide sequence information. Here, we propose PepNet, an interpretable neural network for predicting both AIPs and AMPs by applying a pre-trained protein language model to fully utilize the peptide sequence information. It first captures the information of residue arrangements and physicochemical properties using a residual dilated convolution block, and then seizes the function-related diverse information by introducing a residual Transformer block to characterize the residue representations generated by a pre-trained protein language model. After training and testing, PepNet demonstrates great superiority over other leading AIP and AMP predictors and shows strong interpretability of its learned peptide representations. A user-friendly web server for PepNet is freely available at http://liulab.top/PepNet/server .
Source: Communications Biology
Authors: Jiyun Han, Tongxin Kong, Juntao Liu
Institution: Shandong University
Language: English
Subfield: Microbiology
Field: Immunology and Microbiology
Domain: Life Sciences
Open Access status: gold
Estimated APC paid: $3,890
Awards: G2263236428, G79062576
OpenAlex ID: W4402949285