文献检索文档翻译深度研究
Suppr Zotero 插件Zotero 插件
邀请有礼套餐&价格历史记录

新学期,新优惠

限时优惠:9月1日-9月22日

30天高级会员仅需29元

1天体验卡首发特惠仅需5.99元

了解详情
不再提醒
插件&应用
Suppr Zotero 插件Zotero 插件浏览器插件Mac 客户端Windows 客户端微信小程序
高级版
套餐订阅购买积分包
AI 工具
文献检索文档翻译深度研究
关于我们
关于 Suppr公司介绍联系我们用户协议隐私条款
关注我们

Suppr 超能文献

核心技术专利:CN118964589B侵权必究
粤ICP备2023148730 号-1Suppr @ 2025

AttnTAP: A Dual-input Framework Incorporating the Attention Mechanism for Accurately Predicting TCR-peptide Binding.

作者信息

Xu Ying, Qian Xinyang, Tong Yao, Li Fan, Wang Ke, Zhang Xuanping, Liu Tao, Wang Jiayin

机构信息

Department of Computer Science and Technology, School of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, China.

Geneplus Beijing Institute, Beijing, China.

出版信息

Front Genet. 2022 Aug 22;13:942491. doi: 10.3389/fgene.2022.942491. eCollection 2022.


DOI:10.3389/fgene.2022.942491
PMID:36072653
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC9441555/
Abstract

T-cell receptors (TCRs) are formed by random recombination of genomic precursor elements, some of which mediate the recognition of cancer-associated antigens. Due to the complicated process of T-cell immune response and limited biological empirical evidence, the practical strategy for identifying TCRs and their recognized peptides is the computational prediction from population and/or individual TCR repertoires. In recent years, several machine/deep learning-based approaches have been proposed for TCR-peptide binding prediction. However, the predictive performances of these methods can be further improved by overcoming several significant flaws in neural network design. The interrelationship between amino acids in TCRs is critical for TCR antigen recognition, which was not properly considered by the existing methods. They also did not pay more attention to the amino acids that play a significant role in antigen-binding specificity. Moreover, complex networks tended to increase the risk of overfitting and computational costs. In this study, we developed a dual-input deep learning framework, named AttnTAP, to improve the TCR-peptide binding prediction. It used the bi-directional long short-term memory model for robust feature extraction of TCR sequences, which considered the interrelationships between amino acids and their precursors and postcursors. We also introduced the attention mechanism to give amino acids different weights and pay more attention to the contributing ones. In addition, we used the multilayer perceptron model instead of complex networks to extract peptide features to reduce overfitting and computational costs. AttnTAP achieved high areas under the curves (AUCs) in TCR-peptide binding prediction on both balanced and unbalanced datasets (higher than 0.838 on McPAS-TCR and 0.908 on VDJdb). Furthermore, it had the highest average AUCs in TPP-I and TPP-II tasks compared with the other five popular models (TPP-I: 0.84 on McPAS-TCR and 0.894 on VDJdb; TPP-II: 0.837 on McPAS-TCR and 0.893 on VDJdb). In conclusion, AttnTAP is a reasonable and practical framework for predicting TCR-peptide binding, which can accelerate identifying neoantigens and activated T cells for immunotherapy to meet urgent clinical needs.

摘要
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/705f/9441555/fff418f9802f/fgene-13-942491-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/705f/9441555/382475f15bf3/fgene-13-942491-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/705f/9441555/20d35bfee137/fgene-13-942491-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/705f/9441555/dace3cae8711/fgene-13-942491-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/705f/9441555/1eedc7c34cc1/fgene-13-942491-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/705f/9441555/fff418f9802f/fgene-13-942491-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/705f/9441555/382475f15bf3/fgene-13-942491-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/705f/9441555/20d35bfee137/fgene-13-942491-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/705f/9441555/dace3cae8711/fgene-13-942491-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/705f/9441555/1eedc7c34cc1/fgene-13-942491-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/705f/9441555/fff418f9802f/fgene-13-942491-g005.jpg

相似文献

[1]
AttnTAP: A Dual-input Framework Incorporating the Attention Mechanism for Accurately Predicting TCR-peptide Binding.

Front Genet. 2022-8-22

[2]
DeepLION2: deep multi-instance contrastive learning framework enhancing the prediction of cancer-associated T cell receptors by attention strategy on motifs.

Front Immunol. 2024

[3]
DeepLION: Deep Multi-Instance Learning Improves the Prediction of Cancer-Associated T Cell Receptors for Accurate Cancer Detection.

Front Genet. 2022-4-11

[4]
An Attention Based Bidirectional LSTM Method to Predict the Binding of TCR and Epitope.

IEEE/ACM Trans Comput Biol Bioinform. 2022

[5]
epiTCR: a highly sensitive predictor for TCR-peptide binding.

Bioinformatics. 2023-5-4

[6]
SETE: Sequence-based Ensemble learning approach for TCR Epitope binding prediction.

Comput Biol Chem. 2020-6-20

[7]
MATHLA: a robust framework for HLA-peptide binding prediction integrating bidirectional LSTM and multiple head attention mechanism.

BMC Bioinformatics. 2021-1-6

[8]
iTCep: a deep learning framework for identification of T cell epitopes by harnessing fusion features.

Front Genet. 2023-5-9

[9]
On TCR binding predictors failing to generalize to unseen peptides.

Front Immunol. 2022

[10]
Attention-aware contrastive learning for predicting T cell receptor-antigen binding specificity.

Brief Bioinform. 2022-11-19

引用本文的文献

[1]
AI-driven epitope prediction: a system review, comparative analysis, and practical guide for vaccine development.

NPJ Vaccines. 2025-8-30

[2]
A roadmap for T cell receptor-peptide-bound major histocompatibility complex binding prediction by machine learning: glimpse and foresight.

Brief Bioinform. 2025-7-2

[3]
Benchmarking of T cell receptor-epitope predictors with ePytope-TCR.

Cell Genom. 2025-6-27

[4]
LightCTL: lightweight contrastive TCR-pMHC specificity learning with context-aware prompt.

Brief Bioinform. 2025-5-1

[5]
[Prediction of MHC II antigen peptide-T cell receptors binding based on foundation model].

Sheng Wu Yi Xue Gong Cheng Xue Za Zhi. 2024-12-25

[6]
TCRcost: a deep learning model utilizing TCR 3D structure for enhanced of TCR-peptide binding.

Front Genet. 2024-10-2

[7]
BertTCR: a Bert-based deep learning framework for predicting cancer-related immune status based on T cell receptor repertoire.

Brief Bioinform. 2024-7-25

[8]
Development and Clinical Applications of Therapeutic Cancer Vaccines with Individualized and Shared Neoantigens.

Vaccines (Basel). 2024-6-27

[9]
Transformers meets neoantigen detection: a systematic literature review.

J Integr Bioinform. 2024-6-1

[10]
Artificial intelligence and neoantigens: paving the path for precision cancer immunotherapy.

Front Immunol. 2024-5-29

本文引用的文献

[1]
DeepLION: Deep Multi-Instance Learning Improves the Prediction of Cancer-Associated T Cell Receptors for Accurate Cancer Detection.

Front Genet. 2022-4-11

[2]
A tale of solving two computational challenges in protein science: neoantigen prediction and protein structure prediction.

Brief Bioinform. 2022-1-17

[3]
NetTCR-2.0 enables accurate prediction of TCR-peptide binding by using paired TCRα and β sequence data.

Commun Biol. 2021-9-10

[4]
DLpTCR: an ensemble deep learning framework for predicting immunogenic peptide recognized by T cell receptor.

Brief Bioinform. 2021-11-5

[5]
TCR Recognition of Peptide-MHC-I: Rule Makers and Breakers.

Int J Mol Sci. 2020-12-23

[6]
Current challenges for unseen-epitope TCR interaction prediction and a new perspective derived from image classification.

Brief Bioinform. 2021-7-20

[7]
Prediction of Specific TCR-Peptide Binding From Large Dictionaries of TCR-Peptide Pairs.

Front Immunol. 2020

[8]
T-cell repertoire analysis and metrics of diversity and clonality.

Curr Opin Biotechnol. 2020-10

[9]
T cell antigen discovery.

Nat Methods. 2021-8

[10]
Comparative study of whole exome sequencing-based copy number variation detection tools.

BMC Bioinformatics. 2020-3-5

文献AI研究员

20分钟写一篇综述,助力文献阅读效率提升50倍

立即体验

用中文搜PubMed

大模型驱动的PubMed中文搜索引擎

马上搜索

推荐工具

医学文档翻译智能文献检索