使用蛋白质语言模型进行蛋白质相互作用热点预测,数据有限
1Institute of Biomedical Sciences, Academia Sinica, Taipei, 115, Taiwan. karen.sarkisyan@gmail.com.
BMC bioinformatics
|March 17, 2024
概括
蛋白质语言模型有效地使用进化数据预测蛋白质与蛋白质相互作用的热点. 这些模型提供了一个更快,更便宜的替代实验,以了解残留物质的特性.
科学领域:
- 计算生物学 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:
- 蛋白质语言模型 (PLM) 灵感来源于人类语言模型,用于分析蛋白质序列.
- PLM在预测蛋白质结构,功能和突变影响方面表现有前途.
- 从有限的数据来预测残留物质的PLM的使用,如蛋白质-蛋白质相互作用 (PPI) 热点,尚未被探索.
研究的目的:
- 调查使用PLM衍生表示作为预测PPI热点特征的可行性.
- 评估基于PLM的方法与传统的序列和基于结构的方法的性能.
主要方法:
- 使用了414个经过实验确认的PPI热点和504个PPI非热点的数据集.
- 使用PLM进行无监督学习,从蛋白质序列中提取特征.
- 应用机器学习模型使用PLM学习的表示来预测PPI热点.
主要成果:
- PLM成功地从进化序列信息中捕获关键的功能残留属性.
- 基于PLM的方法与基于PPI热点预测的序列和结构特征相比,实现了竞争性性能.
- 确定了一个最佳的功能集,平衡信息获取和防止过度装配.
结论:
- 基于变压器的PLM可以从稀疏的数据集中提取有价值的知识,特别是对于具有挑战性的任务,如PPI热点预测.
- PLM为预测某些残留性质提供了实验方法的成本效益和时间效率高的替代方案.
- 需要进一步的研究,以了解驱动残留物质预测特征的可解释性.
更多相关视频
07:08Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
Published on: July 14, 2015
7.3K
08:38Genome-wide Protein-protein Interaction Screening by Protein-fragment Complementation Assay PCA in Living Cells
Published on: March 3, 2015
13.3K
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
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
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
02:40Ligand 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
01:24Protein Organization
6.5K
Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence....
The primary structure of a protein is its amino acid sequence....
6.5K
02:04Protein-Protein Interfaces
3.8K
3.8K