Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, and Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai, 200240, China.
DigitalGene, Ltd, Shanghai, 200240, China.
BMC Bioinformatics. 2023 Nov 13;24(1):430. doi: 10.1186/s12859-023-05562-z.
Antibody-mediated immune responses play a crucial role in the immune defense of human body. The evolution of bioengineering has led the progress of antibody-derived drugs, showing promising efficacy in cancer and autoimmune disease therapy. A critical step of this development process is obtaining the affinity between antibodies and their binding antigens.
In this study, we introduce a novel sequence-based antigen-antibody affinity prediction method, named DG-Affinity. DG-Affinity uses deep neural networks to efficiently and accurately predict the affinity between antibodies and antigens from sequences, without the need for structural information. The sequences of both the antigen and the antibody are first transformed into embedding vectors by two pre-trained language models, then these embeddings are concatenated into an ConvNeXt framework with a regression task. The results demonstrate the superiority of DG-Affinity over the existing structure-based prediction methods and the sequence-based tools, achieving a Pearson's correlation of over 0.65 on an independent test dataset.
Compared to the baseline methods, DG-Affinity achieves the best performance and can advance the development of antibody design. It is freely available as an easy-to-use web server at https://www.digitalgeneai.tech/solution/affinity .
抗体介导的免疫反应在人体的免疫防御中起着至关重要的作用。生物工程学的发展推动了抗体衍生药物的进步，在癌症和自身免疫性疾病治疗中显示出有前景的疗效。这一发展过程的关键步骤是获得抗体与其结合抗原之间的亲和力。
在这项研究中，我们介绍了一种新的基于序列的抗原-抗体亲和力预测方法，名为 DG-Affinity。DG-Affinity 使用深度神经网络从序列中高效、准确地预测抗体与抗原之间的亲和力，而无需结构信息。抗原和抗体的序列首先通过两个预先训练的语言模型转化为嵌入向量，然后将这些嵌入向量连接到一个具有回归任务的 ConvNeXt 框架中。结果表明，DG-Affinity 优于现有的基于结构的预测方法和基于序列的工具，在独立测试数据集上实现了超过 0.65 的 Pearson 相关系数。
与基线方法相比，DG-Affinity 表现出最佳性能，可推进抗体设计的发展。它可以在 https://www.digitalgeneai.tech/solution/affinity 作为一个易于使用的网络服务器免费获得。
