基于相似性重建和自适应组合算法预测药物蛋白相互作用
IEEE transactions on computational biology and bioinformatics
|August 14, 2025
概括
通过准确预测药物蛋白相互作用,CombDPI增强了药物发现. 这种计算方法提高了内省和概括性,在识别潜在相互作用方面表现优于现有的方法.
科学领域:
- 计算生物学是一种计算生物学.
- 药物发现 药物发现
- 生物信息学是一种生物信息学.
背景情况:
- 准确预测药物蛋白相互作用 (DPI) 对于加速药物发现至关重要.
- 现有的计算方法往往难以平衡内省 (识别错误负数) 与可概括性 (对新数据的性能).
研究的目的:
- 开发一种新的计算方法,CombDPI,它解决了预测药物蛋白相互作用的当前方法的局限性.
- 提高数据集内虚假阴性结果的识别和预测对新药或蛋白质的概括性.
主要方法:
- 组合DPI采用了两部分战略:类似性重建用于内省和适应性组合用于预测.
- 它从多个角度重建相似关系,以提高数据集内的预测可靠性.
- 对于新型实体,CombDPI根据与已知的药物/蛋白质的相似性生成表示,提高可扩展性和通用性.
主要成果:
- 与现有方法相比,CombDPI在三个基准数据集中表现出优越的性能.
- 该方法在空间内 (数据集内) 和空间外 (新数据) 预测设置中都显示出了强有力的结果.
- 案例研究证实了CombDPI在发现潜在的新型药物蛋白相互作用方面的能力.
结论:
- 组合DPI有效地预测药物蛋白相互作用,提供更好的内省和概括性.
- 该方法的新方法提高了预测涉及新药或蛋白质的相互作用的可扩展性.
- CombDPI代表了计算药物发现的重大进步,有助于识别潜在的治疗点.
相关概念视频
Protein-protein Interfaces
13.2K
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...
13.2K
Protein 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
Protein-Drug Binding: Determination Methods
304
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...
304
Factors Affecting Protein-Drug Binding: Drug Interactions
275
Drug interactions are a critical aspect of pharmacology and can occur when two or more drugs compete for the same binding site. This competition can result in one drug displacing another, altering the effect of the displaced drug. Drug interactions are complex processes that rely heavily on how much of the displacer drug is present and how strongly it can bind to the same sites as the displaced drug.
Displacement interactions can have varying outcomes, ranging from toxicity to virtually...
Displacement interactions can have varying outcomes, ranging from toxicity to virtually...
275
Protein-Drug Binding: Mechanism and Kinetics
942
Protein-drug binding refers to the interaction between drugs and proteins within the body. This binding process can occur intracellularly, involving drug interactions with enzymes or receptors within cells, or extracellularly, involving plasma proteins in the blood.
Various forces drive these interactions, including hydrogen bonds, hydrophobic interactions, ionic bonds, electrostatic interactions, and van der Waals forces. These bonds enable drugs to bind to specific sites on proteins,...
Various forces drive these interactions, including hydrogen bonds, hydrophobic interactions, ionic bonds, electrostatic interactions, and van der Waals forces. These bonds enable drugs to bind to specific sites on proteins,...
942
Conserved 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


