蛋白质-蛋白质接口:一个图形神经网络方法
Niccolò Pancino1, Caterina Gallegati1, Fiamma Romagnoli1
1Department of Information Engineering and Mathematics, University of Siena, Via Roma, 56, 53100 Siena, Italy.
International journal of molecular sciences
|June 19, 2024
概括
图形神经网络 (GNN) 通过分析蛋白质结构作为图表,有效地预测蛋白质-蛋白质相互作用 (PPI). 这种计算方法为实验方法提供了一个具有成本效益的替代方案,用于识别交互点.
科学领域:
- 计算生物学 计算生物学
- 生物信息学是一种生物信息学.
- 结构生物学 结构生物学
背景情况:
- 蛋白与蛋白相互作用 (PPI) 对细胞功能和分子理解至关重要.
- 用于PPI预测的实验方法通常是昂贵和耗时的.
- 深度学习,特别是图形神经网络 (GNN),提供了一个高效的计算替代方案.
研究的目的:
- 用GNN来建模PPI预测作为一个以节点为重点的二进制分类任务.
- 评估GNN在识别蛋白质接口中的残留物方面的性能.
- 在不同的数据细分度中分析PPI:整个蛋白质,相互作用链和单一链.
主要方法:
- 使用了来自欧洲蛋白质数据库 (PDBe) 的生物数据.
- 采用蛋白质接口,表面和组件 (PISA) 服务进行数据提取.
- 开发了三个不同的数据集 (整个,接口,链) 进行全面分析.
- 应用图形神经网络 (GNN) 用于残留水平接口预测.
主要成果:
- 在预测蛋白质与蛋白质相互作用部位方面,GNN表现出很高的性能.
- 该模型成功地解决了PPI预测任务的三个变体.
- 结果证实了GNN在分析蛋白质结构和相互作用方面的有效性.
结论:
- 图形神经网络为PPI预测提供了强大而高效的计算工具.
- 这种基于GNN的方法增强了我们理解生物系统中的分子相互作用的能力.
- 该研究验证了GNN在各种PPI预测场景中的使用.
相关概念视频
Protein-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
Protein-Protein Interfaces
3.7K
3.7K
Protein Networks
3.9K
An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
3.9K
Protein Organization
6.4K
Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence....
The primary structure of a protein is its amino acid sequence....
6.4K
Ligand Binding Sites
12.8K
Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
12.8K
Conserved Binding Sites
4.2K
Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...
4.2K


