基准测试共同折叠的方法,以预测共价蛋白-连接体复合体的结构
Tong-Han Zhang1, Jin-Tao Zhu2, Zhi-Xian Huang3
1Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China.
Acta pharmacologica Sinica
|January 12, 2026
概括
一个新的基准,CoFD-Bench,评估用于预测共价蛋白-连接体复合结构的方法. 同折叠模型显示出更高的准确性,但速度较慢,而经典对接是稳定的,但对于向的共价抑制剂设计来说不那么精确.
科学领域:
- 药物发现和结构生物学
- 计算化学和生物信息学
背景情况:
- 向共价抑制剂 (TCI) 提供了增强的药物特性,但它们的合理设计具有挑战性.
- 准确预测共价蛋白 - 连接体复杂结构至关重要,但缺乏强大的基准.
- 同折叠方法在生物分子建模中表现有希望,但它们在共价复合体预测中的表现尚未得到充分探索.
研究的目的:
- 介绍CoFD-Bench,这是一个基准数据集,用于评估预测共价蛋白-连接体复合结构的方法.
- 系统地评估共价复杂预测任务上的经典对接和深度学习共折叠模型.
- 提供有关TCI设计当前计算方法的优点和局限性的见解.
主要方法:
- 开发了CoFD-Bench,这是218个共价复合物的数据集.
- 评价了经典的对接工具 (AutoDock-GPU,CovDock,GNINA) 和共同折叠的模型 (AlphaFold3,Chai-1,Boltz-1x). 这是一个很好的例子.
- 评估了连接体RMSD准确性,蛋白质-连接体相互作用恢复,新对的性能和计算效率.
主要成果:
- 共同折叠方法在准确性和相互作用恢复方面优于传统的对接.
- 在新的口袋-联结体对上,共折叠性能下降,而经典方法显示稳定但适度的结果.
- 同折叠方法在计算上比经典方法慢;AlphaFold3显示了通过非共价同折叠识别共价残留的潜力.
结论:
- CoFD-Bench为共价复合预测方法提供了一个严格的评估框架.
- 同折叠模型为TCI设计提供了更高的准确性,但面临着可扩展性的挑战.
- 结果指导未来开发基于共折叠的TCI设计策略和模型改进.
相关概念视频
The Equilibrium Binding Constant and Binding Strength
14.8K
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:
14.8K
Conserved Binding Sites
5.0K
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...
5.0K
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
Protein Organization
9.0K
Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence....
The primary structure of a protein is its amino acid sequence....
9.0K
Protein Folding
126.1K
Overview
126.1K
Protein-protein Interfaces
14.4K
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...
14.4K


