幽灵折叠:使用结构受约束的合成共进化信号准确预测蛋白质结构
Nitesh Mishra1,2, Bryan Briney1,2,3,4,5
1Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037 USA.
bioRxiv : the preprint server for biology
|November 24, 2025
概括
GhostFold从单个序列生成合成多重序列对齐 (伪MSA),使缺乏同类蛋白质的蛋白质能够准确预测蛋白质结构. 这种方法绕过了传统的数据库搜索,提供了一个计算效率高的解决方案.
科学领域:
- 计算结构生物学计算结构生物学
- 在蛋白质折叠中进行深度学习.
- 生物信息学是一种生物信息学.
背景情况:
- 蛋白质结构预测的准确性在很大程度上依赖于多重序列对齐 (MSA).
- 很少或没有同类蛋白质的蛋白质对准确的结构预测具有重大挑战.
- 现有的方法在孤儿蛋白质和超变区的数据稀缺方面扎.
研究的目的:
- 开发一种新的方法,GhostFold,用于从单个氨基酸序列生成结构受约束的合成MSA (伪MSA).
- 为了克服传统的同类学搜索对蛋白质结构预测的局限性.
- 为了能够准确地预测具有有限或没有可识别同类的蛋白质的结构.
主要方法:
- 利用 ProstT5 蛋白质语言模型和 3Di 结构字母.
- 将一个查询序列投射到一个标记化的结构表示中.
- 代反向翻译以产生多样化,折叠一致的合成序列 (伪MSA).
主要成果:
- GhostFold成功地生成了伪MSA,使挑战性目标的高精度结构预测成为可能.
- 性能与现有的基于MSA和基于语言模型的预测指标相匹配或超过.
- 该方法在计算上轻量级,独立于大型序列数据库.
- 在伪MSAs中观察到信心指标 (pLDDT) 与预测准确性的脱.
结论:
- 结构引导的合成MSA可以在蛋白质结构预测中功能性地取代进化数据.
- GhostFold为计算结构生物学中的一个中心限制提供了一个可扩展和可泛化的解决方案.
- 这项工作转向智能序列合成,用于在深度学习模型中编码结构先验.
相关概念视频
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
Conserved Binding Sites
1.9K
1.9K
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 Organization
155.6K
Overview
155.6K
Conservation of Protein Domains Over Different Proteins
14.0K
Protein domains are small structurally independent units that are part of a single amino acid chain. Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...
14.0K
Protein and Protein Structure
86.6K
Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
A protein's shape is critical to its function. For example, an enzyme...
A protein's shape is critical to its function. For example, an enzyme...
86.6K


