一个CNN-LSTM组合模型用于预测蛋白质与蛋白质相互作用的结合部位
概括
预测蛋白质与蛋白质相互作用 (PPI) 位点对于了解疾病至关重要. 一个新的深度学习模型,CLPPIS,通过整合空间和序列蛋白质特征,有效地识别这些网站,优于现有的方法.
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:
- 蛋白与蛋白相互作用 (PPI) 是生物功能的基础.
- 识别PPI位点对于了解蛋白质功能,疾病机制和药物设计至关重要.
- 用于PPI地点识别的实验方法耗时且昂贵.
研究的目的:
- 开发一种用于预测蛋白质与蛋白质相互作用 (PPI) 场所的新型计算模型.
- 解决预测性能和PPI站点预测数据不平衡方面的挑战.
- 利用深度学习来提高PPI网站识别的准确性.
主要方法:
- 提出了基于序列的深度学习模型CLPPIS (CNN-LSTM组合基于PPI网站预测).
- 集成CNN和LSTM组件以捕捉空间和顺序蛋白质特征.
- 利用了一个新的输入特征组,包括7个物理化学,生物物理和统计特征.
- 采用批量加权损失函数来缓解不平衡数据集带来的问题.
主要成果:
- 与现有的最先进的方法相比,CLPPIS模型显示出更高的性能.
- 空间和序列蛋白质特征的整合被证明对PPI位点预测有益.
- 批量加权损失函数有效地减少了不平衡数据的干扰.
结论:
- CLPPIS模型在PPI网站的计算预测方面取得了重大进展.
- 结合多样化的蛋白质特征和先进的深度学习架构,可以提高预测的准确性.
- 这种方法提供了一种更有效,更准确的替代PPI地点识别传统实验方法.
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
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
12.9K
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...
12.9K
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
3.8K
3.8K
00:49Ligand Binding and Linkage
4.8K
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...
4.8K