病毒BindPredict:通过深度学习和蛋白质序列衍生的洞察力,赋予病毒蛋白质-连接物结合站点的权力
A M B Amorim1,2,3,4,5, C Marques-Pereira1,2,3, T Almeida6
1CNC - Center for Neuroscience and Cell Biology, Center for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra 3004-504, Portugal.
GigaScience
|January 24, 2026
概括
ViralBindPredict只使用蛋白序列准确地预测病毒蛋白-连接体结合点,加速抗病毒药物发现而不需要结构数据. 这种深度学习框架有助于快速识别目标和设计药物.
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:
- 药物开发是昂贵和耗时的,需要更快的方法.
- 传统的计算药物发现依赖于结构数据,这些数据通常是不可用的或不准确的.
- 现有的基于结构的方法,包括AlphaFold,难以一致识别关键的连接结位.
研究的目的:
- 开发一个深度学习框架,ViralBindPredict,用于从氨基酸序列直接预测病毒蛋白-连接体结合点.
- 创建第一个大规模的,精心策划的基准数据集,用于控制数据分割的病毒蛋白-配体相互作用.
主要方法:
- 病毒BindPredict集成了Mordred连接体描述器与蛋白质序列嵌入 (ESM2或ProtTrans).
- 采用无结构深度学习方法来学习约束偏好.
- 使用泄漏控制数据分割 (Cluster90%,NoRed90%→Cluster90%,Cluster40%,NoRed90%→Cluster40%) 来确保模型的可靠评估.
主要成果:
- ViralBindPredict证明了直接从序列中准确预测病毒蛋白-连接体结合部位.
- 该框架实现了新联体的高精度回忆,其性能受蛋白质序列背景的影响.
- 多层感知子,特别是具有ESM-2嵌入式,性能优于基线模型.
结论:
- ViralBindPredict为抗病毒发现提供了一个强大的,基于序列的工作流.
- 它可以快速确定目标优先级,复合物重新定位和新的药物设计,即使没有结构信息.
- 引入的基准数据集有助于严格评估病毒蛋白-联结体相互作用预测模型.
相关概念视频
Ligand Binding Sites
14.9K
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...
14.9K
Ligand Binding Sites
8.7K
8.7K
Conserved Binding Sites
5.1K
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...
5.1K
Conserved Binding Sites
1.9K
1.9K
Ligand Binding and Linkage
5.5K
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...
5.5K
Ligand Binding and Linkage
4.0K
4.0K


