曲率增强图形卷积网络用于生物分子相互作用预测.
Cong Shen1,2, Pingjian Ding3, Junjie Wee2
1College of Computer Science and Electronic Engineering, Hunan University, Changsha, 410000, China.
Computational and structural biotechnology journal
|March 1, 2024
概括
我们介绍了一个曲率增强的图形卷积网络 (CGCN),用于预测生物分子相互作用. 这种新的方法通过结合像奥利维埃-里奇曲率这样的几何性质,显著优于现有模型的现实数据.
科学领域:
- 计算生物学是一种计算生物学.
- 网络科学 网络科学
- 机器学习 机器学习
背景情况:
- 几何深度学习在分析非欧几里德数据方面表现出色.
- 将几何见解集成到学习架构中对于性能至关重要.
- 生物分子相互作用预测是计算生物学中的一个关键挑战.
研究的目的:
- 为改进生物分子相互作用预测提出一种新的曲率增强图形卷积网络 (CGCN).
- 利用奥利维埃-里奇曲率 (ORC) 来描述网络的局部几何性质.
- 通过结合几何特征来增强图形卷积网络 (GCN) 的学习能力.
主要方法:
- 开发了一个CGCN模型,利用奥利维埃-里奇曲率 (ORC) 来评估本地网络拓.
- 在消息传递过程中将ORC纳入权重函数以进行特征聚合.
- 在14个真实世界生物分子相互作用网络和模拟数据上验证了CGCN模型.
主要成果:
- CGCN模型实现了最先进的性能,在14个数据集中的13个数据集中表现优于现有模型.
- 与传统GCN模型相比,在模拟数据中的各种网络密度,尺寸和曲率比率中表现出优异的性能.
- 该模型的有效性在不同的网络特征中是稳定的.
结论:
- 拟议的CGCN模型通过结合网络几何学来显著增强生物分子相互作用预测.
- 奥利维埃-里奇曲线是改善生物网络中GCN性能的一个有效特征.
- 在将几何深度学习应用于生物网络分析方面,CGCN代表了一个有前途的进步.
更多相关视频
相关概念视频
Protein-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
Protein 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
Noncovalent Attractions in Biomolecules
50.6K
Noncovalent attractions are associations within and between molecules that influence the shape and structural stability of complexes. These interactions differ from covalent bonding in that they do not involve sharing of electrons.
Four types of noncovalent interactions are hydrogen bonds, van der Waals forces, ionic bonds, and hydrophobic interactions.
Hydrogen bonding results from the electrostatic attraction of a hydrogen atom covalently bonded to a strong-electronegative atom like oxygen,...
Four types of noncovalent interactions are hydrogen bonds, van der Waals forces, ionic bonds, and hydrophobic interactions.
Hydrogen bonding results from the electrostatic attraction of a hydrogen atom covalently bonded to a strong-electronegative atom like oxygen,...
50.6K
Conserved 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
Ligand 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


