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LMPred: predicting antimicrobial peptides using pre-trained language models and deep learning.

作者信息

Dee William

机构信息

Department of Bioinformatics, School of Biological and Behavioural Sciences, Queen Mary University of London, London E1 4NS, UK.

出版信息

Bioinform Adv. 2022 Mar 31;2(1):vbac021. doi: 10.1093/bioadv/vbac021. eCollection 2022.


DOI:10.1093/bioadv/vbac021
PMID:36699381
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC9710646/
Abstract

MOTIVATION: Antimicrobial peptides (AMPs) are increasingly being used in the development of new therapeutic drugs in areas such as cancer therapy and hypertension. Additionally, they are seen as an alternative to antibiotics due to the increasing occurrence of bacterial resistance. Wet-laboratory experimental identification, however, is both time-consuming and costly, so models are now commonly used in order to screen new AMP candidates. RESULTS: This paper proposes a novel approach for creating model inputs; using pre-trained language models to produce contextualized embeddings, representing the amino acids within each peptide sequence, before a convolutional neural network is trained as the classifier. The results were validated on two datasets-one previously used in AMP prediction research, and a larger independent dataset created by this paper. Predictive accuracies of 93.33% and 88.26% were achieved, respectively, outperforming previous state-of-the-art classification models. AVAILABILITY AND IMPLEMENTATION: All codes are available and can be accessed here: https://github.com/williamdee1/LMPred_AMP_Prediction. SUPPLEMENTARY INFORMATION: Supplementary data are available at online.

摘要
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b054/9710646/4a4068db2132/vbac021f2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b054/9710646/cb07108edc19/vbac021f1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b054/9710646/4a4068db2132/vbac021f2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b054/9710646/cb07108edc19/vbac021f1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b054/9710646/4a4068db2132/vbac021f2.jpg

相似文献

[1]
LMPred: predicting antimicrobial peptides using pre-trained language models and deep learning.

Bioinform Adv. 2022-3-31

[2]
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[5]
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[7]
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[8]
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[9]
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[10]
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引用本文的文献

[1]
AI-guided discovery and optimization of antimicrobial peptides through species-aware language model.

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[2]
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[3]
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[4]
Protein Sequence Analysis landscape: A Systematic Review of Task Types, Databases, Datasets, Word Embeddings Methods, and Language Models.

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[5]
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Chem Sci. 2025-2-20

[6]
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[7]
MFP-MFL: Leveraging Graph Attention and Multi-Feature Integration for Superior Multifunctional Bioactive Peptide Prediction.

Int J Mol Sci. 2025-2-4

[8]
AI Methods for Antimicrobial Peptides: Progress and Challenges.

Microb Biotechnol. 2025-1

[9]
Accelerating antimicrobial peptide design: Leveraging deep learning for rapid discovery.

PLoS One. 2024-12-20

[10]
AutoPeptideML: a study on how to build more trustworthy peptide bioactivity predictors.

Bioinformatics. 2024-9-2

本文引用的文献

[1]
Deep-AmPEP30: Improve Short Antimicrobial Peptides Prediction with Deep Learning.

Mol Ther Nucleic Acids. 2020-6-5

[2]
Antimicrobial peptide identification using multi-scale convolutional network.

BMC Bioinformatics. 2019-12-23

[3]
PTPD: predicting therapeutic peptides by deep learning and word2vec.

BMC Bioinformatics. 2019-9-6

[4]
DRAMP 2.0, an updated data repository of antimicrobial peptides.

Sci Data. 2019-8-13

[5]
A New Method of RNA Secondary Structure Prediction Based on Convolutional Neural Network and Dynamic Programming.

Front Genet. 2019-5-22

[6]
Clustering huge protein sequence sets in linear time.

Nat Commun. 2018-6-29

[7]
Deep learning improves antimicrobial peptide recognition.

Bioinformatics. 2018-8-15

[8]
AmPEP: Sequence-based prediction of antimicrobial peptides using distribution patterns of amino acid properties and random forest.

Sci Rep. 2018-1-26

[9]
DeepSF: deep convolutional neural network for mapping protein sequences to folds.

Bioinformatics. 2018-4-15

[10]
MLACP: machine-learning-based prediction of anticancer peptides.

Oncotarget. 2017-8-19

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