AMP-BERT: Prediction of antimicrobial peptide function based on a BERT model

被引:51
作者
Lee, Hansol [1 ]
Lee, Songyeon [1 ]
Lee, Ingoo [1 ]
Nam, Hojung [1 ,2 ]
机构
[1] Gwangju Inst Sci & Technol GIST, Sch Elect Engn & Comp Sci, Gwangju, South Korea
[2] Gwangju Inst Sci & Technol, AI Grad Sch, 123 Cheomdangwagi Ro, Gwangju 61005, South Korea
基金
新加坡国家研究基金会;
关键词
antimicrobial peptides; antimicrobial resistance; BERT; deep learning; drug discovery; machine learning; sequence classification; transformer; CD-HIT; PROTEIN; THIONINS;
D O I
10.1002/pro.4529
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
Antimicrobial resistance is a growing health concern. Antimicrobial peptides (AMPs) disrupt harmful microorganisms by nonspecific mechanisms, making it difficult for microbes to develop resistance. Accordingly, they are promising alternatives to traditional antimicrobial drugs. In this study, we developed an improved AMP classification model, called AMP-BERT. We propose a deep learning model with a fine-tuned didirectional encoder representations from transformers (BERT) architecture designed to extract structural/functional information from input peptides and identify each input as AMP or non-AMP. We compared the performance of our proposed model and other machine/deep learning-based methods. Our model, AMP-BERT, yielded the best prediction results among all models evaluated with our curated external dataset. In addition, we utilized the attention mechanism in BERT to implement an interpretable feature analysis and determine the specific residues in known AMPs that contribute to peptide structure and antimicrobial function. The results show that AMP-BERT can capture the structural properties of peptides for model learning, enabling the prediction of AMPs or non-AMPs from input sequences. AMP-BERT is expected to contribute to the identification of candidate AMPs for functional validation and drug development. The code and dataset for the fine-tuning of AMP-BERT is publicly available at .
引用
收藏
页数:13
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