对生物分子相互作用的以蛋白质为中心的预测因子进行全面的审查:从蛋白质到核酸,再到其他领域
Pengzhen Jia1, Fuhao Zhang1,2, Chaojin Wu1
1School of Computer Science and Engineering, Central South University, 932 Lushan Road(S), Changsha 410083, China.
Briefings in bioinformatics
|May 13, 2024
概括
预测蛋白质-连接体相互作用对于药物发现至关重要. 这篇评论分析了160多种计算方法,突出了深度学习.
科学领域:
- 生物化学和分子生物学
- 计算生物学 计算生物学
- 药理学 药理学是指药理学的学科.
背景情况:
- 蛋白质-连接体相互作用是生物过程的基础,如基因表达和信号转导.
- 准确识别这些相互作用对于理解分子机制和开发新疗法至关重要.
- 传统的实验方法用于识别蛋白质 - 配体相互作用往往是耗时且昂贵的.
研究的目的:
- 提供现有的计算蛋白质 - 连接物相互作用预测器的全面审查和分析.
- 根据其输入数据,特征表示,建模技术和可用性,对160多个预测器进行分类和评估.
- 识别当前的趋势和新兴的方法在计算蛋白质-连接体相互作用预测领域.
主要方法:
- 系统的文献搜索和数据收集蛋白质 - 配体相互作用预测方法.
- 预测因子被分为四种主要类型:蛋白质-蛋白质,蛋白质-核酸,蛋白质-和蛋白质-其他连接体相互作用.
- 预测特征的比较分析,包括输入数据 (序列,结构),特征提取,机器学习模型和可访问性.
主要成果:
- 该综述涵盖了160多种不同的蛋白质-连接体相互作用预测因子.
- 目前的方法主要利用蛋白质序列,进化信息是关键特征.
- 深度学习方法已经显著提高了预测准确度,这代表了该领域的重大进展.
结论:
- 深度学习方法已经彻底改变了蛋白质-连接体相互作用预测的准确性.
- 新兴趋势包括基于序列的预训练模型的开发和结构信息的整合.
- 这种全面的分析为计算生物学和药物发现研究人员提供了宝贵的资源.
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相关概念视频
02:04Protein-protein Interfaces
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 polypeptide...
01:49Conserved Binding Sites
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 analyses the...
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 analyses the...
02:26Protein Networks
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,...
01:24Protein Organization
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.
02:04Protein-Protein Interfaces
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 polypeptide...
02:26Protein Networks
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,...