ABTrans: A Transformer-based Model for Predicting Interaction between Anti-Aβ Antibodies and Peptides.

IF 3.9 2区 生物学 Q1 MATHEMATICAL & COMPUTATIONAL BIOLOGY
Yuhong Su, Xincheng Zeng, Lingfeng Zhang, Yanlin Bian, Yangjing Wang, Buyong Ma
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引用次数: 0

Abstract

Antibodies against Aβ peptide have been recently approved to treat Alzheimer's disease, underscoring the importance of understanding their interactions for developing more potent treatments. Here we investigated the interaction between anti-Aβ antibodies and various peptides using a deep learning model. Our model, ABTrans, was trained on dodecapeptide sequences from phage display experiments and known anti-Aβ antibody sequences sourced from public sources. It classified the binding ability between anti-Aβ antibodies and dodecapeptides into four levels: not binding, weak binding, medium binding, and strong binding, achieving an accuracy of 0.83. Using ABTrans, we examined the cross-reaction of anti-Aβ antibodies with other human amyloidogenic proteins, revealing that Aducanumab and Donanemab exhibited the least cross-reactivity. Additionally, we systematically screened interactions between eleven selected anti-Aβ antibodies and all human proteins to identify potential off-target candidates.

ABTrans:基于变压器的抗 Aβ 抗体与多肽相互作用预测模型
针对 Aβ 肽的抗体最近已被批准用于治疗阿尔茨海默病,这凸显了了解它们之间的相互作用对于开发更有效的治疗方法的重要性。在此,我们使用深度学习模型研究了抗Aβ抗体与各种肽之间的相互作用。我们的模型 ABTrans 是根据噬菌体展示实验中的十二肽序列和来自公共资源的已知抗 Aβ 抗体序列训练而成的。它将抗 Aβ 抗体与十二肽的结合能力分为四个等级:不结合、弱结合、中等结合和强结合,准确率达到 0.83。利用 ABTrans,我们检测了抗 Aβ 抗体与其他人类淀粉样蛋白的交叉反应,结果发现 Aducanumab 和 Donanemab 的交叉反应最小。此外,我们还系统地筛选了 11 种选定的抗 Aβ 抗体与所有人类蛋白质之间的相互作用,以确定潜在的脱靶候选者。
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来源期刊
Interdisciplinary Sciences: Computational Life Sciences
Interdisciplinary Sciences: Computational Life Sciences MATHEMATICAL & COMPUTATIONAL BIOLOGY-
CiteScore
8.60
自引率
4.20%
发文量
55
期刊介绍: Interdisciplinary Sciences--Computational Life Sciences aims to cover the most recent and outstanding developments in interdisciplinary areas of sciences, especially focusing on computational life sciences, an area that is enjoying rapid development at the forefront of scientific research and technology. The journal publishes original papers of significant general interest covering recent research and developments. Articles will be published rapidly by taking full advantage of internet technology for online submission and peer-reviewing of manuscripts, and then by publishing OnlineFirstTM through SpringerLink even before the issue is built or sent to the printer. The editorial board consists of many leading scientists with international reputation, among others, Luc Montagnier (UNESCO, France), Dennis Salahub (University of Calgary, Canada), Weitao Yang (Duke University, USA). Prof. Dongqing Wei at the Shanghai Jiatong University is appointed as the editor-in-chief; he made important contributions in bioinformatics and computational physics and is best known for his ground-breaking works on the theory of ferroelectric liquids. With the help from a team of associate editors and the editorial board, an international journal with sound reputation shall be created.
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