预测ncRNA-蛋白相互作用与图表注意力模型利用个性化的子图
Fatemeh Khoushehgir1, Zahra Noshad1
1Department of IT and Computer Engineering, Azarbaijan Shahid Madani University, Tabriz, Iran.
Journal of bioinformatics and computational biology
|December 5, 2025
概括
预测非编码RNA (ncRNA) 和蛋白质相互作用对于理解基因调节和疾病至关重要. 一种新方法使用个性化的子图和图注意力网络来更准确地预测ncRNA-蛋白相互作用.
科学领域:
- 生物信息学是一种生物信息学.
- 计算生物学 计算生物学
- 基因组学就是基因组学.
背景情况:
- 准确预测非编码RNA (ncRNA) 和蛋白质相互作用对于基因调节,疾病机制阐明和治疗开发至关重要.
- 机器学习,特别是图形神经网络 (GNN),通过分析分子数据结构来预测这些相互作用.
- 现有的GNN方法经常使用固定跳转子图,这可能会限制它们捕获复杂相互作用模式的能力,并省略相关的分子信息.
研究的目的:
- 开发一种新的计算方法,以更好地预测ncRNA-蛋白相互作用.
- 克服目前GNN方法中固定跳转子图分析的局限性.
- 通过整合序列和结构特征来提高ncRNA-蛋白相互作用预测的准确性和可扩展性.
主要方法:
- 使用个性化的子图选择框架,在潜在的交互站点周围提取最有信息的子图.
- 使用图表注意网络 (GAT) 来从这些个性化子图中学习节点表示.
- 序列级特征是使用k-mer频率捕获的,而结构信息是通过node2vec嵌入体现的.
主要成果:
- 与现有方法相比,拟议的方法在预测ncRNA-蛋白相互作用方面取得了显著的改进.
- 该算法保持了可接受的计算复杂性,使其适合大规模数据集.
- 通过个性化子图集集成序列和结构特征可以提高预测准确性.
结论:
- 使用个性化子图和GAT的新方法为ncRNA-蛋白相互作用预测提供了更准确和可扩展的解决方案.
- 这种方法通过超越固定跳转子图的限制,有效地捕捉到各种交互模式.
- 这些发现有助于推进基因调节,疾病机制和药物发现方面的研究.
相关概念视频
02:26Protein Networks
4.5K
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,...
4.5K
02:26Protein Networks
2.8K
2.8K
02:04Protein-protein Interfaces
14.4K
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...
14.4K
02:40Ligand Binding Sites
14.8K
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...
14.8K
01:49Conserved Binding Sites
5.0K
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...
5.0K