DSSGNN-PPI:一种基于双结构和序列图神经网络的蛋白质-蛋白质相互作用预测模型
Fan Zhang1, Sheng Chang2, Binjie Wang3
1Huaihe Hospital of Henan University, Kaifeng 475004, China; School of Computer and Information Engineering, Henan University, Kaifeng 475004, China.
Computers in biology and medicine
|June 4, 2024
概括
本研究介绍了DSSGNN-PPI,这是一种用于预测蛋白质与蛋白质相互作用 (PPI) 的新型图形神经网络模型. 它有效地结合了结构和序列数据,以提高PPI预测的准确性.
科学领域:
- 计算生物学 计算生物学
- 结构生物学 结构生物学
- 生物信息学是一种生物信息学.
背景情况:
- 通过实验验证蛋白质与蛋白质相互作用 (PPI) 是资源密集的.
- 准确预测PPI对于理解细胞机制至关重要.
研究的目的:
- 开发一种有效和准确的方法来预测蛋白质与蛋白质相互作用 (PPI).
- 利用图形神经网络 (GNN) 来整合蛋白质结构和序列信息.
主要方法:
- 为PPI设计了一个新的双结构和序列GNN (DSSGNN-PPI) 模型.
- 从氨基酸残留物构建了一个距离图,并使用图的注意网络来学习结构嵌入.
- 获得了基于序列的嵌入,并融合了结构和序列特征.
- 采用一个封闭的图表注意力网络,从融合的特征中学习复杂的拓模式.
主要成果:
- DSSGNN-PPI在提高多种类型蛋白质与蛋白质相互作用的预测方面表现出了显著的有效性.
- 该模型成功地整合了异构的多源信息,以改善PPI理解.
- 多层次代表学习和信息融合策略被证明是有效的.
结论:
- DSSGNN-PPI为解决结构生物学中的复杂问题提供了一个新的范式,特别是PPI预测.
- 开发的框架为提高蛋白相互作用网络的预测准确性提供了有效的解决方案.
- 该源代码在GitHub上公开提供,以便进一步研究和应用.
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 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
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
Protein-Protein Interfaces
3.7K
3.7K
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
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


