签署的两个空间近距离模型用于蛋白质-蛋白质相互作用网络中的学习表示
Nikolaos Nakis1, Chrysoula Kosma2, Anastasia Brativnyk3
1École Polytechnique, LIX, Institute Polytechnique de Paris, Palaiseau, 91120, France.
Bioinformatics (Oxford, England)
|April 23, 2025
概括
我们开发了一个新的模型,Signed Two-Space Proximity Model (S2-SPM),以更准确地预测蛋白质与蛋白质相互作用 (PPI). S2-SPM分析了激活和抑制相互作用,改善了我们对生物过程的理解.
科学领域:
- 计算生物学 计算生物学
- 系统生物学 系统生物学
- 生物信息学是一种生物信息学.
背景情况:
- 预测蛋白质与蛋白质相互作用 (PPI) 对理解生物过程和疾病至关重要.
- 测定PPI的实验方法是昂贵的;机器学习提供了一个替代方案.
- 签名PPI网络,包括激活和抑制相互作用,需要专门的分析.
研究的目的:
- 为分析已签名的PPI网络引入签名的两个空间近距离模型 (S2-SPM).
- 开发一种明确区分正和负蛋白相互作用的模型.
- 在这些网络中识别代表极端蛋白质配置文件的原型.
主要方法:
- 利用两个独立的潜空间,单独建模正负相互作用.
- 通过在这些潜伏空间中的接近来表示蛋白质相似性.
- 使用链接预测任务和基因本体学 (GO) 丰富分析进行验证.
主要成果:
- 与基线方法相比,S2-SPM在预测相互作用存在和信号方面表现出卓越的性能.
- 丰富分析证实了已识别的原型及其相关的生物任务的生物学相关性.
- 统计学意义,灵敏度分析和BNMI指标证实了模型的稳定性和可靠性.
结论:
- 通过结合签名的PPI,S2-SPM准确地模拟了生物系统中复杂的调节机制.
- 该模型提供了对不同相互作用类型的功能作用的洞察,并确定了关键蛋白质原型.
- 在S2-SPM是免费的,促进进一步的研究在签名网络分析.
相关概念视频
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
02:26Protein 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
02:04Protein-Protein Interfaces
3.7K
3.7K
01:49Conserved 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
02:40Ligand 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
01:57Protein Complexes with Interchangeable Parts
1.8K
1.8K