一种端到端的方法,用于预测化合物-蛋白质相互作用,基于简化的同质图形卷积网络和预训练的语言模型
Yufang Zhang1,2,3, Jiayi Li4, Shenggeng Lin4
1School of Mathematical Sciences and SJTU-Yale Joint Center for Biostatistics and Data Science, Shanghai Jiao Tong University, Shanghai, 200240, China.
Journal of cheminformatics
|June 7, 2024
概括
我们开发了SPVec-SGCN-CPI,这是一种用于预测化合物-蛋白质相互作用的新型深度学习方法. 这种方法优于不平衡的数据,加速药物发现和目标识别.
科学领域:
- 计算生物学是一种计算生物学.
- 生物信息学是一种生物信息学.
- 药物发现 药物发现
背景情况:
- 确定化合物-蛋白相互作用 (CPI) 对药物发现和理解蛋白质功能至关重要.
- 深度学习模型提供高效,高通量CPI预测,减少对昂贵实验的依赖.
- 现有的方法经常与现实世界生物数据集中常见的固有数据不平衡作斗争.
研究的目的:
- 引入SPVec-SGCN-CPI,这是一个端到端的深度学习方法,用于准确预测化合物-蛋白质相互作用.
- 解决CPI预测中的数据不平衡和计算效率的挑战.
- 通过现有的最先进的方法来验证模型的性能.
主要方法:
- 使用简化图形卷积网络 (SGCN) 模型与 SPVec.ec 的低维特征集成.
- 采用图形拓信息与节点特征一起用于交互预测.
- 集成层级传播,以高效聚合K级邻居信息,减轻邻居爆炸.
主要成果:
- 在三个数据集中,SPVec-SGCN-CPI显著超过了四种机器学习和六种深度学习方法.
- 该模型表现出卓越的性能,特别是在数据不平衡的场景中.
- 在未标记的ChEMBL数据上进行了验证的预测,通过分子对接和现有证据证实了排名最高的相互作用.
结论:
- SPVec-SGCN-CPI可靠地预测化合物-蛋白相互作用,为药物重新描述和发现提供了强大的工具.
- 该方法有效地将化合物和蛋白质的异质信息融合在一起.
- 这种方法通过考虑样本不平衡和计算效率来加快目标识别和简化药物发现.
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