基于结构的神经网络蛋白质-碳水化合物相互作用预测在残留水平
Samuel W Canner1, Sudhanshu Shanker2, Jeffrey J Gray1,2
1Program in Molecular Biophysics, The Johns Hopkins University, Baltimore, MD, United States.
Frontiers in bioinformatics
|July 6, 2023
概括
我们开发了两个深度学习模型,CAPSIF:V和CAPSIF:G,以识别蛋白质上的碳水化合物结合位点. CAPSIF:V表现出卓越的性能,在实验和预测的蛋白质结构上准确预测这些关键的相互作用点.
科学领域:
- 计算生物学是一种计算生物学.
- 结构生物信息学 结构生物信息学
- 机器学习在药物发现中的作用
背景情况:
- 碳水化合物与蛋白质的相互作用对于细胞的识别和分化等过程至关重要.
- 由于缺乏可靠的计算工具,预测这些相互作用是具有挑战性的.
- 目前用于识别碳水化合物结合部位的现有方法有限.
研究的目的:
- 开发新的深度学习模型,用于预测蛋白质上的碳水化合物结合点.
- 为此任务比较不同深度学习架构的性能.
- 评估这些模型对预测的蛋白质结构的有用性.
主要方法:
- 开发了两个深度学习模型:一个3D-UNet (CAPSIF:V) 和一个等效图形神经网络 (CAPSIF:G).
- 训练并评估了预测非共价碳水化合物结合位点的模型.
- 在实验确定和AlphaFold2预测的蛋白质结构上测试模型性能.
主要成果:
- 两种CAPSIF:V和CAPSIF:G模型都超过了先前的碳水化合物结合部位预测方法.
- 与CAPSIF:G (Dice分数0.543,MCC0.538) 相比,CAPSIF:V获得了更高的准确性 (子得分0.597,MCC0.599).
- 在实验确定和AlphaFold2预测的蛋白质结构上,CAPSIF:V显示了相当的性能.
结论:
- CAPSIF模型提供可靠的计算工具,用于预测碳水化合物结合部位.
- CAPSIF:V是一个高效的模型,即使在预测的蛋白质结构上也表现良好.
- 这些模型可以增强用于预测蛋白质-碳水化合物复杂结构的甘氨酸对接协议.
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