VN-EGNN:E(3)-和SE(3)-等价图形神经网络与虚拟节点增强蛋白质结合部位识别
Florian Sestak1, Lisa Schneckenreiter2, Johannes Brandstetter3,4
1ELLIS Unit Linz and LIT AI Lab, Institute for Machine Learning, Johannes Kepler University Linz, Altenberger Straße 69, Linz, 4040, Austria. sestak@ml.jku.at.
Journal of cheminformatics
|December 16, 2025
概括
我们开发了VN-EGNN,这是一种新的图形神经网络方法,用于识别蛋白质结合部位. 这种方法显著提高了药物发现的准确性和理解蛋白质-连接体相互作用.
科学领域:
- 计算生物学是一种计算生物学.
- 结构生物信息学 结构生物信息学
- 机器学习在药物发现中的作用
背景情况:
- 精确识别蛋白质结合部位对于药物发现和理解分子相互作用至关重要.
- 传统的图形神经网络 (GNN) 在模拟结合口袋的复杂3D几何学方面面临着挑战.
- 开发新的计算方法对于在这个领域推进预测性能至关重要.
研究的目的:
- 引入VN-EGNN,一种用于增强绑定站点识别的新方法.
- 用图形神经网络来改进复杂的几何实体的建模,如结合口袋.
- 为了生成蛋白质结合部位的精确神经表示.
主要方法:
- 将虚拟节点集成到E{n}-和SE{n}-等效图形神经网络 (EGNNs) 中.
- 在EGNN框架内扩展消息传递方案.
- 对基准数据集的评估:COACH420,HOLO4K和PDBbind2020用于绑定网站中心本地化.
主要成果:
- VN-EGNN在多个数据集中建立了一个新的最先进的绑定网站中心识别技术.
- 与现有方法相比,DCC/DCA成功率明显改善.
- 在绑定站点本地化预测性能方面取得了重大进展.
结论:
- VN-EGNN提供了一种强大的新工具,用于精确识别绑定位置.
- 该方法显示了加速药物发现管道的巨大潜力.
- 通过改进的几何建模,VN-EGNN通过改进的几何建模推进了蛋白质-连接体相互作用的研究.
相关概念视频
Ligand 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
Ligand Binding Sites
8.5K
8.5K
Conserved 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
Protein-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
Ligand Binding and Linkage
5.4K
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...
5.4K
Protein 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


