PLMAM-PLA:一种使用预训练的语言模型和注意力机制来预测蛋白质 - 连接物结合 afinity 的方法
IEEE transactions on computational biology and bioinformatics
|August 14, 2025
概括
我们开发了PLMAM-PLA,这是一种新的深度学习模型,用于仅使用蛋白序列和连接体结构来预测蛋白质-连接体结合亲和力. 这种基于序列的方法为药物发现应用提供了更有效的替代方案.
科学领域:
- 计算生物学是一种计算生物学.
- 药物发现 药物发现
- 生物信息学是一种生物信息学.
背景情况:
- 蛋白质 - 配体结合亲和力对药物发现和酶动力学至关重要.
- 当前的深度学习模型通常需要复杂的结构数据.
- 基于序列的预测提供了一个更实用,更有效的方法.
研究的目的:
- 开发一种基于序列的新型深度学习模型,用于预测蛋白质-连接体结合亲和力.
- 提高绑定亲和度预测方法的效率和可访问性.
- 利用预训练的语言模型进行增强的特征提取.
主要方法:
- 开发了基于序列的深度学习模型PLMAM-PLA.
- 利用预训练的语言模型 (ESM-2,MolFormer) 来从蛋白质序列和连接体SMILES中提取特征.
- 使用扩展卷积神经网络,SKNets,SENets和注意力机制进行特征增强和融合.
主要成果:
- 仅使用序列和SMILES数据,PLMAM-PLA有效地预测了蛋白质-连接体结合亲和力.
- 废弃性研究证实了单个模型组件的贡献.
- 可视化实验证明了有效的特征表示捕获.
- 与最先进的方法相比,案例研究显示出强烈的概括性和优越的性能.
结论:
- PLMAM-PLA提供了一种强大而有效的工具,用于基于序列的蛋白质-连接体结合亲和力预测.
- 该模型展示了卓越的性能和概括能力.
- 这种方法简化了用于药物发现和相关领域的绑定亲和性预测.
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