关于深度学习方法和工具的调查,用于预测蛋白质结合部位
Alina Rohulia1, Yanli Wang2, Jianlin Cheng3
1Department of Chemical and Biomedical Engineering, University of Missouri, Columbia, MO, USA.
Methods in molecular biology (Clifton, N.J.)
|July 29, 2025
概括
深度学习 (DL) 显著提高了蛋白质结合部位预测的准确性. 本综述详细介绍了最先进的DL方法,指导研究人员开发人工智能驱动的生物相互作用分析工具.
科学领域:
- 生物化学 生物化学
- 计算生物学 计算生物学
- 人工智能的人工智能
背景情况:
- 蛋白质与多种连接体相互作用,对细胞功能至关重要.
- 准确预测蛋白质结合部位对于理解生物相互作用至关重要.
- 深度学习 (DL) 已经成为增强绑定站点预测准确性的强大工具.
研究的目的:
- 为预测蛋白质结合部位提供最先进的深度学习方法的全面审查.
- 为开发和实施DL模型在这个领域提供详细的指南.
- 编译和评估最近的DL方法,包括模型类型,数据和指标.
主要方法:
- 编译和评估最近关于DL的文献,以预测蛋白质结合部位.
- 讨论数据收集,预处理和数据库的使用 (UniProt,Dockground,PDBbind).
- 探索著名的DL架构,如卷积神经网络 (CNN) 和图形神经网络 (GNN).
主要成果:
- 确定DL模型开发的关键细节:模型类型,输入/输出数据,数据库和评估指标.
- 展示各种数据库用于训练DL模型的实用性.
- 对CNN和GNN用于绑定站点预测的进步的概述.
结论:
- 深度学习方法在预测蛋白质结合部位方面取得了重大进展.
- 这篇评论为研究人员提供了DL技术和资源的知识,以推进人工智能驱动的预测.
- 通过准确的结合部位预测来了解蛋白质-连接体相互作用对于生物研究至关重要.
相关概念视频
01:49Conserved Binding Sites
4.4K
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...
4.4K
02:40Ligand Binding Sites
13.2K
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...
13.2K
02:04Protein-protein Interfaces
13.3K
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...
13.3K
01:22Protein-Drug Binding: Determination Methods
308
Determining protein-drug binding can be achieved through indirect and direct methods, each providing valuable insights into the interaction between proteins and drugs.
Indirect methods involve isolating the bound drug from its free form in biological samples such as blood, serum, or plasma. These techniques aim to measure the percentage of drugs bound to proteins. Equilibrium dialysis is a commonly used method where the free drug concentration at equilibrium is measured by separating the bound...
Indirect methods involve isolating the bound drug from its free form in biological samples such as blood, serum, or plasma. These techniques aim to measure the percentage of drugs bound to proteins. Equilibrium dialysis is a commonly used method where the free drug concentration at equilibrium is measured by separating the bound...
308
00:49Ligand Binding and Linkage
4.9K
Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked. In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence...
4.9K
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