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AOPxSVM:一种使用块替换矩阵以及氨基酸组成、转化和分布嵌入来识别抗氧化肽的支持向量机。

AOPxSVM: A Support Vector Machine for Identifying Antioxidant Peptides Using a Block Substitution Matrix and Amino Acid Composition, Transformation, and Distribution Embeddings.

作者信息

Li Rujun, Wang Haotian, Yu Qiunan, Cai Jing, Jiang Liangzhen, Luo Ximei, Zou Quan, Lv Zhibin

机构信息

College of Biomedical Engineering, Sichuan University, Chengdu 610041, China.

College of Food and Biological Engineering, Chengdu University, Chengdu 610106, China.

出版信息

Foods. 2025 Jun 6;14(12):2014. doi: 10.3390/foods14122014.


DOI:10.3390/foods14122014
PMID:40565623
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC12192177/
Abstract

Antioxidant peptides (AOPs) have the natural properties of food preservatives; they are capable of improving the oxidation stability of food while also providing additional benefits such as disease prevention. Traditional experimental methods for identifying antioxidant peptides are time consuming and costly, so effective machine learning models are increasingly being valued by researchers. In this study, we integrated amino acid composition, transformation, and distribution (CTD) and block substitution matrix 62 (BLOSUM62) to develop an SVM-based AOP prediction model called AOPxSVM. This strategy significantly improves the prediction accuracy of the model by comparing 15 feature combinations and feature selection strategies, with their effectiveness being visually verified using UMAP. AOPxSVM achieves high accuracy values of 0.9092 and 0.9330, as well as Matthew's correlation coefficients (MCCs) of 0.8253 and 0.8670, on two independent test sets, both surpassing the state-of-the-art methods based on the same test sets, thus demonstrating AOPs' excellent identification capability. We believe that AOPxSVM can serve as a powerful tool for identifying AOPs.

摘要

抗氧化肽(AOPs)具有食品防腐剂的天然特性;它们能够提高食品的氧化稳定性,同时还能提供诸如疾病预防等额外益处。传统的抗氧化肽鉴定实验方法既耗时又昂贵,因此有效的机器学习模型越来越受到研究人员的重视。在本研究中,我们整合了氨基酸组成、转化和分布(CTD)以及块替换矩阵62(BLOSUM62),以开发一种基于支持向量机的AOP预测模型,称为AOPxSVM。通过比较15种特征组合和特征选择策略,该策略显著提高了模型的预测准确率,其有效性通过UMAP进行了直观验证。AOPxSVM在两个独立测试集上分别实现了0.9092和0.9330的高精度值,以及0.8253和0.8670的马修斯相关系数(MCCs),均超过了基于相同测试集的现有最佳方法,从而证明了AOPs出色的识别能力。我们相信AOPxSVM可以作为识别AOPs的有力工具。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/648e/12192177/4ff8ca2fbfb7/foods-14-02014-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/648e/12192177/3bda249ba8cc/foods-14-02014-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/648e/12192177/5a4d4be2a3b1/foods-14-02014-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/648e/12192177/61a9924aa69b/foods-14-02014-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/648e/12192177/4ff8ca2fbfb7/foods-14-02014-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/648e/12192177/3bda249ba8cc/foods-14-02014-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/648e/12192177/5a4d4be2a3b1/foods-14-02014-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/648e/12192177/61a9924aa69b/foods-14-02014-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/648e/12192177/4ff8ca2fbfb7/foods-14-02014-g004.jpg

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本文引用的文献

[1]
PMPred-AE: a computational model for the detection and interpretation of pathological myopia based on artificial intelligence.

Front Med (Lausanne). 2025-3-13

[2]
High-Accuracy Identification and Structure-Activity Analysis of Antioxidant Peptides via Deep Learning and Quantum Chemistry.

J Chem Inf Model. 2025-1-27

[3]
Accurate RNA velocity estimation based on multibatch network reveals complex lineage in batch scRNA-seq data.

BMC Biol. 2024-12-18

[4]
Dual function antioxidant and anti-inflammatory fish maw peptides: Isolation and structure-activity analysis via tandem molecular docking and quantum chemical calculation.

Food Chem. 2025-2-15

[5]
RetroCaptioner: beyond attention in end-to-end retrosynthesis transformer via contrastively captioned learnable graph representation.

Bioinformatics. 2024-9-2

[6]
A Foundation Model Identifies Broad-Spectrum Antimicrobial Peptides against Drug-Resistant Bacterial Infection.

Nat Commun. 2024-8-30

[7]
Identification of microbe-disease signed associations via multi-scale variational graph autoencoder based on signed message propagation.

BMC Biol. 2024-8-15

[8]
PEL-PVP: Application of plant vacuolar protein discriminator based on PEFT ESM-2 and bilayer LSTM in an unbalanced dataset.

Int J Biol Macromol. 2024-10

[9]
MTMol-GPT: De novo multi-target molecular generation with transformer-based generative adversarial imitation learning.

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[10]
msBERT-Promoter: a multi-scale ensemble predictor based on BERT pre-trained model for the two-stage prediction of DNA promoters and their strengths.

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