FoldExplorer:使用序列增强图形嵌入快速准确的蛋白质结构搜索
Yuan Liu1, Ying Zhang1, Zhen Zhou1
1Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, and Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai 200240, China.
Journal of molecular biology
|September 1, 2025
概括
这项新型深度学习方法FoldExplorer有效地搜索大量的蛋白质结构数据库. 它准确地识别了类似的蛋白质结构,甚至低信心的预测,推进了结构生物学研究.
科学领域:
- 结构生物学
- 生物信息学
- 计算生物学
背景情况:
- 由于精确的预测方法,蛋白质结构数据库正在迅速扩大.
- 有效和精确的蛋白质结构搜索越来越重要.
- 传统的对齐方法在大规模的数据库搜索中遇到了困难.
研究的目的:
- 开发一种新的深度学习方法,以高效准确地搜索蛋白质结构.
- 解决大规模数据库应用中的传统方法的局限性.
- 提供蛋白质结构空间的全面视图以获得新的见解.
主要方法:
- 开发了一种深度学习模型FoldExplorer,利用图形注意力神经网络和蛋白质语言模型.
- 共同编码结构和序列信息以产生专门的嵌入.
- 对几何相似性搜索和分类任务的评估性能.
主要成果:
- FoldExplorer表现出具有竞争力的性能,接近传统的对齐工具.
- 在搜索和分类方面表现优于最近的深度学习和基于序列的方法.
- 在搜索低可信度预测结构方面表现出有效性.
- 在大规模的数据库搜索中表现出高效率.
结论:
- 在大型数据库中寻找蛋白质结构的高效准确解决方案.
- 该模型的嵌入提供了蛋白质结构空间的全面视图,使得新的见解成为可能.
- FoldExplorer是推动结构生物学和蛋白质宇宙研究的重要工具.
相关概念视频
Protein Organization
7.0K
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....
7.0K
Protein and Protein Structures
10.8K
10.8K
Protein Families
15.7K
Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism. Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members. If these new proteins contain similar amino acids in key...
15.7K
Protein and Protein Structure
81.2K
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...
81.2K
Globular and Fibrous Proteins
44.4K
Many proteins can be classified into two distinct subtypes - globular or fibrous. These two types differ in their shapes and solubilities.
Globular proteins are also known as spheroproteins and typically are approximately round in shape. They contain a mix of amino acid types and contain differing sequences in their primary structures. Globular proteins have many different functions, such as enzymes, cellular messengers, and molecular transporters. These roles often require the proteins to be...
Globular proteins are also known as spheroproteins and typically are approximately round in shape. They contain a mix of amino acid types and contain differing sequences in their primary structures. Globular proteins have many different functions, such as enzymes, cellular messengers, and molecular transporters. These roles often require the proteins to be...
44.4K
Protein Complexes with Interchangeable Parts
2.6K
Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order...
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order...
2.6K


