增强卷积神经网络用于使用序列特征扩展预测蛋白质-蛋白质相互作用
IEEE transactions on computational biology and bioinformatics
|August 14, 2025
概括
一种新的多通道编码方法提高了蛋白质-蛋白质相互作用 (PPI) 预测的准确性. 这种方法通过整合基本和高级序列特征来改进CNN模型,优于现有方法.
科学领域:
- 计算生物学是一种计算生物学.
- 生物信息学是一种生物信息学.
- 机器学习在生物学中的应用
背景情况:
- 蛋白与蛋白相互作用 (PPI) 对生物功能和理解细胞机制至关重要.
- 准确预测PPI对于破译蛋白质功能和作用机制至关重要.
- 现有的蛋白序编码方法在捕获复杂相互作用特征方面存在局限性.
研究的目的:
- 提出针对卷积神经网络 (CNN) 量身定制的蛋白质序列的新型多通道编码策略.
- 增强CNN模型的特征抽象能力,以改善PPI预测.
- 为了验证拟议的编码方法与既有技术的有效性.
主要方法:
- 开发了一种新的多通道编码方法,包含基本的序列信息和额外的特征,如氨基酸含量和局部碎片.
- 将编码应用于CNN模型,用于预测蛋白质-蛋白质相互作用.
- 在涉及16,470种蛋白质的718,306种PPI的大数据集上进行了5倍交叉验证实验.
- 使用分子对接和丰富分析验证的预测.
主要成果:
- 拟议的编码方法比原来的SSC编码表现出了8.46%的性能改进.
- 与现有文献方法相比,实现了4.13%-10.88%的更好的表现.
- 该模型在交叉验证中达到94.35%的准确性和0.8871的马修斯相关系数 (MCC).
- 分子对接和丰富分析支持预测的PPI的生物相关性.
结论:
- 新的多通道编码显著提高了CNN在预测蛋白质-蛋白质相互作用方面的性能.
- 拟议的方法提供了改进的特征抽象和预测准确性,超过了当前的基准.
- 这种方法为开发先进的PPI识别技术和改进预测方法提供了宝贵的见解.
相关概念视频
02:04Protein-protein Interfaces
13.2K
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...
13.2K
02:26Protein Networks
4.1K
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,...
4.1K
02:26Conservation of Protein Domains Over Different Proteins
11.4K
Protein domains are small structurally independent units that are part of a single amino acid chain. Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...
11.4K
02:04Protein-Protein Interfaces
3.8K
3.8K
01:57Protein Complexes with Interchangeable Parts
2.6K
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...
2.6K
02:41Protein Complex Assembly
2.1K
2.1K