在没有实验结构的情况下,对计算工具进行系统评估,以预测突变对蛋白质-连接体结合亲和力的影响
Qisheng Pan1,2, Stephanie Portelli1,2, Thanh Binh Nguyen1,2
1The Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Cooper Rd, St Lucia, Brisbane, QLD 4067, Australia.
Briefings in bioinformatics
|February 5, 2026
概括
预测药物耐药性突变需要了解蛋白质 - 配体结合亲和力变化. 像AlphaFold这样的当前蛋白质模型在评估这些突变时显示性能下降,这表明需要突变意识的计算方法.
科学领域:
- 计算生物学是一种计算生物学.
- 结构生物信息学 结构生物信息学
- 药物发现 药物发现
背景情况:
- 由于突变而导致的耐药性是一种主要的健康问题.
- 了解突变对蛋白质-配体结合的影响至关重要.
- 蛋白质结构预测方面的进展 (例如,AlphaFold) 需要对突变影响分析进行评估.
研究的目的:
- 评估当前蛋白质建模工具 (AlphaFold2,AlphaFold3,同质模型) 在预测突变诱导的蛋白质-连接体结合亲缘关系变化的有用性.
- 将不同计算模型的性能与实验结构进行比较,以预测突变效应.
主要方法:
- 评估各种基于突变的方法和评分功能.
- 使用计算机生成的蛋白质-配体复合体.
- 从AlphaFold2,AlphaFold3和同质模型对实验数据的预测的比较.
主要成果:
- 与实验结构相比,在计算模型中观察到5%-30%的性能下降.
- AlphaFold3和实验结构显示出类似的性能下降 (~5%).
- 阿尔法Fold2和同质模型表现出更大的性能损失 (10% - 30%),特别是在接口突变和小连接体.
结论:
- 虽然AlphaFold模型提供了准确的结构,但它们缺乏突变特定的动态信息.
- 目前的模型在预测突变诱导的结合亲和力变化方面存在局限性.
- 为了可靠的in silico药物耐药性分析,需要补充突变意识的方法.
相关概念视频
Ligand Binding Sites
15.1K
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...
15.1K
Ligand Binding Sites
8.8K
8.8K
Ligand Binding and Linkage
5.6K
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...
5.6K
Ligand Binding and Linkage
4.1K
4.1K
Conserved Binding Sites
5.2K
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...
5.2K
The Equilibrium Binding Constant and Binding Strength
15.1K
The equilibrium binding constant (Kb) quantifies the strength of a protein-ligand interaction. Kb can be calculated as follows when the reaction is at equilibrium:
15.1K


