用AI模型预测药物与蛋白结合强度,助力精准药物设计。
Binding Affinity Prediction: From Conventional to Machine Learning-Based Approaches
- 结合传统机器学习与深度学习方法预测结合亲和力
- 利用蛋白质与小分子数据提升预测准确率
- 适合药物研发与生物机制研究者参考
蛋白-配体结合是小分子(如药物或抑制剂)与靶标蛋白结合的过程。结合亲和力表征生物分子间相互作用的强弱,在治疗设计、蛋白质工程、酶优化及生物机制解析中至关重要。过去几十年中,大量工作致力于结合亲和力预测。本文综述近期重要进展,聚焦方法、评估策略与基准数据集。我们观察到传统机器学习与深度学习模型在该领域应用日益广泛,同时蛋白质与类药物小分子数据量持续增长。随着预测性能提升以及美国FDA逐步淘汰动物实验,以人工智能虚拟细胞(AIVCs)为代表的无实验模拟模型有望推动结合亲和力预测发展;反过来,结合亲和力预测的进步也可优化AIVCs。未来研究可进一步提升时间动态模拟、细胞类型特异性与多组学整合能力,支持更精确、个性化的生物学预测。
原文摘要 · Abstract (English)
Protein-ligand binding is the process by which a small molecule (drug or inhibitor) attaches to a target protein. Binding affinity, which characterizes the strength of biomolecular interactions, is essential for tackling diverse challenges in life sciences, including therapeutic design, protein engineering, enzyme optimization, and elucidating biological mechanisms. Much work has been devoted to predicting binding affinity over the past decades. Here, we review recent significant works, with a focus on methods, evaluation strategies, and benchmark datasets. We note growing use of both traditional machine learning and deep learning models for predicting binding affinity, accompanied by an increasing amount of data on proteins and small drug-like molecules. With improved predictive performance and the FDA's phasing out of animal testing, AI-driven in silico models, such as AI virtual cells (AIVCs), are poised to advance binding affinity prediction; reciprocally, progress in building binding affinity predictors can refine AIVCs. Future efforts in binding affinity prediction and AI-driven in silico models can enhance the simulation of temporal dynamics, cell-type specificity, and multi-omics integration to support more accurate and personalized outcomes.
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