图形PBSP:基于图形注意力网络和预训练模型ProstT5的蛋白质结合部位预测
Xiaohan Sun1, Zhixiang Wu1, Jingjie Su1
1College of Chemistry and Life Science, Beijing University of Technology, Beijing 100124, China.
International journal of biological macromolecules
|October 29, 2024
概括
使用新的序列和结构特征,GraphPBSP准确地预测了蛋白质-蛋白质/结位. 这种先进的图形注意力网络模型为蛋白质工程和药物设计提供了更好的洞察力.
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:
- 蛋白质与蛋白质/的相互作用对于生物过程至关重要.
- 准确预测结合点的位置至关重要,但具有挑战性.
- 现有的方法需要改进,以提高预测准确度.
研究的目的:
- 开发一个有效的计算模型来预测蛋白质-蛋白质/结位.
- 引入新的功能和方法来改进绑定站点预测.
- 为蛋白质工程和药物设计提供一种有价值的工具.
主要方法:
- 开发了GraphPBSP,这是一个利用图形注意网络,卷积神经网络和多层感知器的模型.
- 集成了多种特征:接口残留物双向倾向,ProstT5序列嵌入,物理化学性质和结构特征.
- 实施了基于空间邻居的特征统计方法和用于增强学习的多尺度目标函数.
主要成果:
- 在蛋白质-蛋白质/结位预测方面,GraphPBSP显著优于现有的最先进方法.
- 该模型在蛋白质-DNA/RNA结合部位预测任务上表现出强大的概括能力.
- 像 ProstT5 嵌入式和残留物双向倾向等新功能有助于提高性能.
结论:
- 图形PBSP是一个非常有效和有前途的方法,用于绑定网站预测.
- 该模型的性能突显了集成序列和结构特征的实用性.
- GraphPBSP为推进蛋白质工程和药物发现工作提供了宝贵的见解.
相关概念视频
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
12.7K
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...
12.7K
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
00:49Ligand Binding and Linkage
4.8K
Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked. In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence...
4.8K
01:24Protein Organization
6.3K
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....
6.3K