通过流量匹配来适应基于结构的蛋白质-蛋白质对接的共同折叠模型
Da Xu1, Lee-Shin Chu1, Jeffrey J Gray1
1Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA.
bioRxiv : the preprint server for biology
|December 11, 2025
概括
我们开发了AF2Dock,这是一种基于结构的新型蛋白质-蛋白质对接方法,适应了共折叠模型. AF2Dock在预测抗体-抗原复合体方面表现出色,优于纳米体目标的现有方法.
科学领域:
- 计算生物学是一种计算生物学.
- 结构生物学是结构生物学.
- 生物信息学是一种生物信息学.
背景情况:
- 像AlphaFold这样的共同折叠模型在蛋白质复合体预测方面表现出色,但在缺乏多个序列对齐 (MSA) 的目标上扎.
- 基于结构的蛋白质-蛋白质对接提供了一个替代方案,通过预测没有MSAs的未结合单体的结合结构.
研究的目的:
- 为了适应基于结构的蛋白质-蛋白质对接的共同折叠模型.
- 通过修改AlphaFold-Multimer (AF-M) 来开发一个名为AF2Dock的生成对接模型.
主要方法:
- 用一个对接模块替换了AF-M的模板模块.
- 使用流程匹配目标,对修改后的模型进行端到端的训练.
- 将该方法应用于AF-M的OpenFold实现,创建了AF2Dock.
主要成果:
- AF2Dock在使用非holo输入的PINDER-AF2基准和抗体/纳米体数据集上展示了具有竞争力的性能.
- AF2Dock超越了对纳米体复合体的所有测试对接方法.
- AF2Dock提供了直角预测,成功地解决了共同折叠模型失败的情况.
结论:
- AF2Dock代表了基于结构的蛋白质-蛋白质对接的共同折叠模型的新适应.
- 全参数微调对于AF-M组件在对接中的性能至关重要.
- 该研究强调了将共同折叠架构集成到对接策略中的潜力和局限性.
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