PepBAN:深度学习框架与双线注意力和对抗性学习用于蛋白相互作用预测
Shuaiyan Li1, Xiaorui Wang1, Yuchen Zhu1
1College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.
Journal of chemical information and modeling
|August 25, 2025
概括
PepBAN是一个深度学习框架,使用ESM-2等先进模型准确预测蛋白相互作用 (PepPI). 它在概括和解释相互作用机制方面表现出色,优于线性和循环的现有方法.
科学领域:
- 计算生物学
- 生物化学
- 药物发现
背景情况:
- 蛋白相互作用 (PepPIs) 对于治疗和疫苗至关重要.
- 由于结构和结合亲和数据有限,通过计算来预测PepPI具有挑战性.
- 现有的模型与一般化和新结构, 如循环.
研究的目的:
- 开发一个强大的深度学习框架PepBAN,用于准确的蛋白相互作用预测.
- 增强不同蛋白质标的模型概括性,特别是在稀疏的结合数据中.
- 使PepPI机制的解释和解决周期性相互作用的挑战.
主要方法:
- 使用蛋白质语言模型ESM-2进行蛋白质和的表征.
- 采用条件域对抗性学习来提高概括性.
- 开发了一个双线性注意网络 (BAN) 来模拟本地相互作用并确定关键残留物.
- 结合了非正规氨基酸的循环的原子解析分子图方法.
主要成果:
- 在基准数据集上,PepBAN显著优于最先进的模型.
- 在预测循环与蛋白质相互作用方面表现出卓越的性能.
- 通过注意力权重分析来解释相互作用机制的能力.
- 在循环中成功处理非正规氨基酸,这是先前方法的关键局限性.
结论:
- PepBAN提供了一个强大且可解释的深度学习解决方案,用于蛋白相互作用的预测.
- 该框架促进了基于的治疗方法和疫苗的开发.
- 对于药物发现,PepBAN在探索循环的化学空间方面提供了明显的优势.
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