融合结构与序列信息,提升抗体-抗原相互作用预测精度
Multi-Modality Representation Learning for Antibody-Antigen Interactions Prediction
- 结合3D结构与1D序列数据,捕捉抗体内部层级关系
- 在自建基准数据集上超越现有最佳模型性能
- 适合药物设计与免疫学研究者参考
尽管深度学习在抗体-抗原相互作用(AAI)预测中发挥关键作用,但公开可用的序列-结构配对数据稀缺,限制了模型泛化能力。现有方法多关注残基级静态细节,忽略抗体的细粒度结构表征及其相互间相似性。为此,我们提出一种多模态表征方法,融合3D结构与1D序列数据,揭示抗体内部的层次化关系。基于此,构建了MuLAAIP框架,利用图注意力网络捕捉图级别结构特征,并采用归一化自适应图卷积网络建模抗体间序列关联。此外,我们构建了一个包含结构、序列信息及相互作用标签的AAI基准数据集。在该数据集上的大量实验表明,MuLAAIP在预测性能上优于当前最先进方法。代码与数据集已公开于https://github.com/trashTian/MuLAAIP以支持可复现性。
原文摘要 · Abstract (English)
While deep learning models play a crucial role in predicting antibody-antigen interactions (AAI), the scarcity of publicly available sequence-structure pairings constrains their generalization. Current AAI methods often focus on residue-level static details, overlooking fine-grained structural representations of antibodies and their inter-antibody similarities. To tackle this challenge, we introduce a multi-modality representation approach that integates 3D structural and 1D sequence data to unravel intricate intra-antibody hierarchical relationships. By harnessing these representations, we present MuLAAIP, an AAI prediction framework that utilizes graph attention networks to illuminate graph-level structural features and normalized adaptive graph convolution networks to capture inter-antibody sequence associations. Furthermore, we have curated an AAI benchmark dataset comprising both structural and sequence information along with interaction labels. Through extensive experiments on this benchmark, our results demonstrate that MuLAAIP outperforms current state-of-the-art methods in terms of predictive performance. The implementation code and dataset are publicly available at https://github.com/trashTian/MuLAAIP for reproducibility.
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