GNNGL-PPI:使用基于全球图和局部子图的图形神经网络对蛋白质-蛋白质相互作用的多类预测
Xin Zeng1, Fan-Fang Meng1, Meng-Liang Wen2
1College of Mathematics and Computer Science, Dali University, 671003, Dali, China.
BMC genomics
|May 9, 2024
概括
本研究介绍了GNNGL-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方法. GNNGL-PPI提高了多类PPI预测的准确性,为传统实验方法提供了更有效的替代方案.
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.
- 网络科学 网络科学
背景情况:
- 蛋白与蛋白相互作用 (PPI) 是生物过程,疾病机制和治疗发展的基础.
- 准确识别PPI类别和提高计算预测准确度是重大挑战.
- 现有的PPI预测计算方法经常与多类别分类和不平衡的数据集扎.
研究的目的:
- 开发一种新的计算方法,用于精确预测蛋白质与蛋白质相互作用的多类别.
- 解决处理复杂的PPI数据和不平衡的类分布的现有方法的局限性.
- 为了提高生物和临床应用中预测蛋白质-蛋白质相互作用的效率和可靠性.
主要方法:
- 拟议的GNNGL-PPI是一种图形神经网络方法,使用图形同态网络 (GIN) 进行全球图形特征和GIN As Kernel (GIN-AK) 进行本地子图形特征.
- 整合了不对称损失 (ASL) 功能,以管理不同PPI类别的不平衡样本分布.
- 在使用随机,BFS和DFS分区算法对六个基准数据集进行了GNNGL-PPI评估.
主要成果:
- 与最先进的多类型PPI预测方法相比,GNNGL-PPI表现优越,F1测量证明了这一点.
- 该方法在识别特定类别的蛋白质-蛋白质相互作用方面取得了高准确性.
- 解释性分析证实了GNNGL-PPI在预测蛋白质与蛋白质相互作用方面的可靠性和有效性.
结论:
- GNNGL-PPI为多类蛋白质-蛋白质相互作用预测提供了强大而准确的解决方案.
- 全球和本地图形特征的整合,以及ASL,显著提高了预测能力.
- 这种计算方法通过改进PPI识别,为推动生物研究和药物发现提供了有价值的工具.
更多相关视频
06:50Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions
Published on: January 26, 2024
1.8K
08:38Genome-wide Protein-protein Interaction Screening by Protein-fragment Complementation Assay PCA in Living Cells
Published on: March 3, 2015
13.3K
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
3.8K
3.8K
01:30Classification of Neurotransmitters
2.8K
Neurotransmitters play a crucial role in the communication between neurons in the autonomic nervous system. Neurons in the autonomic nervous system can be cholinergic or adrenergic depending on the neurotransmitters synthesized. Cholinergic neurons use acetylcholine as their primary neurotransmitter. This includes all the preganglionic fibers of the sympathetic and pre- and postganglionic fibers of the parasympathetic nervous systems. In addition, neurons of the somatic nervous system also use...
2.8K
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
02:40Ligand 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