将分子粗粒度模型集成到几何表示学习框架中,用于蛋白质-蛋白质复合体性质预测
Yang Yue1, Shu Li2, Yihua Cheng1
1School of Computer Science, The University of Birmingham, Edgbaston, Birmingham, UK.
Nature communications
|November 7, 2024
概括
我们开发了MCGLPPI,这是一种使用粗粒度模型和图形神经网络来预测蛋白质-蛋白质相互作用特性的新方法. 这种方法是高效和准确的,性能优于原子和残留量级的方法,计算成本更低.
科学领域:
- 计算生物学 计算生物学
- 结构生物信息学 结构生物信息学
- 机器学习 机器学习
背景情况:
- 预测蛋白质与蛋白质相互作用 (PPI) 特性对于理解生物过程和开发疾病治疗至关重要.
- 当前基于结构的机器学习方法通常使用原子或残留尺度表示,这可能是计算密集的,可能会错过关键的交互细节.
研究的目的:
- 引入MCGLPPI,一个新的几何表示学习框架,用于准确和高效地预测PPI属性.
- 评估MCGLPPI的性能与现有的原子和残留量级方法相比.
主要方法:
- MCGLPPI将图形神经网络 (GNN) 与马丁分子粗粒度 (CG) 模型相结合.
- 该框架使用CG尺度表示来预测PPI属性.
- 研究了蛋白质域-域相互作用结构的预训,以提高预测能力.
主要成果:
- 与原子和残留尺度方法相比,MCGLPPI在三个下游PPI属性预测任务上取得了竞争性表现.
- 在MCGLPPI的CG尺度方法消耗的计算资源只有三分之一.
- 用CG规模进行预训练,提高了PPI任务的预测性能.
结论:
- MCGLPPI提供了一种有效和高效的解决方案,用于在粗粒度尺度上预测PPI属性.
- 这个框架为大规模的生物分子相互作用分析提供了一个有前途的工具.
- 该研究强调了在机器学习中粗粒度表示对于PPI预测的优点.
相关概念视频
02:27Predicting Molecular Geometry
34.1K
VSEPR Theory for Determination of Electron Pair Geometries
34.1K
01:57Protein Complexes with Interchangeable Parts
2.5K
Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order...
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order...
2.5K
02:00Molecular Models
37.9K
Physical models representing molecular architectures of chemical compounds play essential roles in understanding chemistry. The use of molecular models makes it easier to visualize the structures and shapes of atoms and molecules.
37.9K
02:04Protein-Protein Interfaces
3.7K
3.7K
02:04Protein-protein Interfaces
12.5K
Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a...
12.5K
02:41Protein Complex Assembly
10.6K
Proteins can form homomeric complexes with another unit of the same protein or heteromeric complexes with different types. Most protein complexes self-assemble spontaneously via ordered pathways, while some proteins need assembly factors that guide their proper assembly. Despite the crowded intracellular environment, proteins usually interact with their correct partners and form functional complexes.
Many viruses self-assemble into a fully functional unit using the infected host cell to...
Many viruses self-assemble into a fully functional unit using the infected host cell to...
10.6K