CSI:对比数据层分化用于相互作用预测及其应用于化合物-蛋白相互作用预测的应用
Apurva Kalia1, Dilip Krishnan2, Soha Hassoun1,3
1Department of Computer Science, Tufts University, Medford, MA 02155, United States.
Bioinformatics (Oxford, England)
|July 25, 2023
概括
我们介绍了互动预测的对比分层 (CSI),这是一个新的分区数据方法,以改善互动预测. 通过创建对比学习的多视图,CSI增强了深度学习模型,在药物发现等领域显著提高了预测准确性.
科学领域:
- 计算生物学 计算生物学
- 机器学习 机器学习
- 生物信息学是一种生物信息学.
背景情况:
- 准确预测生物实体 (例如,化合物-蛋白质) 之间的相互作用对于药物发现和合成生物学至关重要.
- 当前的深度学习模型往往难以充分利用交互数据集中固有的关系信息.
- 利用交互对象的多视图表示可以通过对比学习来提高模型性能.
研究的目的:
- 开发一种新的方法,即互动预测对比分层 (CSI),用于分割互动数据集.
- 通过对比学习,通过使用一致和非一致的数据视图来改善对象表示的学习.
- 将CSI应用于化合物-蛋白相互作用预测问题,以加速药物发现和相关应用.
主要方法:
- 通过为每个数据点分配一个关键和多个视图,CSI对数据集进行分层 (分区).
- 在特定密钥下的数据分区形成一致的视图,允许对比的多视图编码.
- 该方法学习了嵌入式,可以在这些一致视图中最大限度地增加相互信息.
主要成果:
- 在化合物-蛋白相互作用预测中,CSI显著提高了平均精度,当使用化合物/序列作为关键时,收益从13.7%到39%不等.
- 当在酶数据集中使用反应特征作为关键时,观察到16.9%至63%的进一步增长.
- 这些结果表明了数据分层和对比学习对相互作用预测的有效性.
结论:
- 通过有效利用多视图数据表示,CSI提供了一种强大的方法来增强交互预测.
- 该方法显示了与缺乏数据分层和对比学习的基线模型相比的显著改进.
- CSI有可能加速药物发现,代谢工程和合成生物学应用.
相关概念视频
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
4.0K
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,...
4.0K
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
02:04Protein-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
02:26Conservation of Protein Domains Over Different Proteins
10.9K
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...
10.9K