从静态结构到动态结构:通过基于图形的深度学习改进绑定亲和度预测
Yaosen Min1, Ye Wei1, Peizhuo Wang1,2
1Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, 100084, China.
Advanced science (Weinheim, Baden-Wurttemberg, Germany)
|August 29, 2024
概括
这项研究介绍了Dynaformer,这是一种使用分子动力学模拟来预测蛋白质 - 连接体结合亲和力的深度学习模型. Dynaformer 实现了最先进的性能,通过识别有前途的药物化合物来加速药物发现.
科学领域:
- 计算化学和化学信息学
- 结构生物学和药物设计.
- 在分子建模中的人工智能.
背景情况:
- 准确预测蛋白质 - 配体结合亲缘关系对于基于结构的药物设计至关重要.
- 目前的数据驱动方法受到依赖静态蛋白质结构的限制,忽视了动态结合组合.
- 分子动力学 (MD) 模拟提供了一种方法来近似这些动态组合.
研究的目的:
- 开发一种深度学习模型,利用MD模拟进行增强的蛋白质 - 连接体结合亲缘关系预测.
- 评估模型在基准数据集和虚拟选应用中的性能.
- 通过改进的计算预测,加速药物发现的早期阶段.
主要方法:
- 策划了一个MD数据集,包含3218个蛋白质 - 配体复合体.
- 开发了基于图形的深度学习模型Dynaformer,以从MD轨迹中学习.
- 应用Dynaformer对CASF-2016基准数据集进行评分和排名评估.
- 对热冲击蛋白90 (HSP90) 和实验验证的打击化合物进行虚拟选.
主要成果:
- 在CASF-2016基准上,Dynaformer展示了最先进的评分和排名能力.
- 该模型在结合亲缘关系预测方面表现优于之前报告的方法.
- 虚拟查确定了20个HSP90候选化合物,其中12个被验证为命中,包括新的支架.
结论:
- 通过整合MD模拟和深度学习,Dynaformer可以有效地预测蛋白质-连接体结合亲和力.
- 该模型显示了加速虚拟药物查和早期药物发现过程的重大前景.
- 这种方法提供了一个强大的计算工具,用于识别新药候选药物.
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