一种特征提取免费的方法,用于从共同化数据中推断蛋白质相互作用体的推断
Yu-Hsin Chen1,2,3, Kuan-Hao Chao3, Jin Yung Wong3
1Bioinformatics Program, Taiwan International Graduate Program, National Taiwan University, Taipei 106, Taiwan.
Briefings in bioinformatics
|June 16, 2023
概括
SPIFFED通过使用一种新的深度学习方法,增强了从共分化质谱数据中发现蛋白质复合物的能力. 这种方法减少了偏差,并提高了预测蛋白质-蛋白质相互作用和复合物的准确性.
科学领域:
- 蛋白质组学是指蛋白质组学.
- 系统生物学 系统生物学
- 计算生物学 计算生物学
背景情况:
- 蛋白质复合体对于细胞功能至关重要.
- 与质谱学 (CF-MS) 结合的同分离是一种研究蛋白质复合体的高通量方法.
- 对于CF-MS数据分析的现有计算方法面临着假阳性,特征偏差和不平衡数据的挑战.
研究的目的:
- 从CF-MS数据开发一种新的计算框架,用于精确的蛋白质-蛋白质相互作用 (PPI) 和蛋白质复合体预测.
- 克服现有方法的局限性,包括手工制作的特征偏差和不平衡数据问题.
- 为了提高互动组推断的灵敏度和可靠性.
主要方法:
- 开发SPIFFED (用特征提取自由化数据预测交互原子的软件),这是一个端到端的深度学习架构.
- 使用卷积神经网络集成原始CF-MS化数据.
- 实施平衡的培训策略和整体方法,以改善预测.
- 使用ClusterONE进行高可信度蛋白质复合体推断.
主要成果:
- 在PPI预测方面,SPIFFED的表现优于最先进的方法,特别是在不平衡的培训条件下.
- 使用平衡数据进行SPIFFED培训显著提高了对真正PPI的敏感性.
- 集成的SPIFFED模型提供了多个CF-MS数据集的强大集成.
- 该软件有助于推断针对实验设计的高可靠性蛋白质复合体.
结论:
- SPIFFED提供了一种强大,无偏见和准确的方法来分析CF-MS数据.
- 没有特征提取的深度学习架构有效地预测蛋白质-蛋白质相互作用和复合体.
- SPIFFED代表了计算蛋白质组学在理解细胞机械方面取得的重大进展.
相关概念视频
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
02:04Protein-protein Interfaces
12.6K
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...
12.6K
01:20Immunoprecipitation
5.6K
Immunoprecipitation, or IP, is a widely used technique that employs protein-antibody interactions to isolate proteins or protein complexes in their native state for studying protein-protein interactions, quaternary structures, or supramolecular complexes. Various modifications of the technique, including chromatin IP, cross-linking IP, and fluorescence IP, are commonly used.
Chromatin Immunoprecipitation
Chromatin immunoprecipitation, also known as ChIP, is used to study protein-DNA or...
Chromatin Immunoprecipitation
Chromatin immunoprecipitation, also known as ChIP, is used to study protein-DNA or...
5.6K
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