融合PDB:人类融合蛋白质的知识库
Himansu Kumar1, Lin-Ya Tang1, Chengyuan Yang2
1Department of Bioinformatics and Systems Medicine, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.
Nucleic acids research
|October 23, 2023
概括
FusionPDB提供了人类融合蛋白序列和3D结构的全面数据库,有助于开发向癌症治疗方法. 这个资源解决了理解新药发现的融合蛋白质的关键差距.
科学领域:
- 计算生物学和生物信息学
- 结构生物学是结构生物学.
- 癌症基因组学 癌症基因组学
背景情况:
- 由基因融合产生的融合蛋白在瘤发生和其他细胞过程中起着重要作用.
- 向融合蛋白具有治疗潜力,但缺乏序列和结构数据阻碍了药物开发.
- 现有的资源缺乏关于人类融合蛋白的完整序列和3D结构的全面信息.
研究的目的:
- 开发人类融合蛋白的计算管道和资源.
- 提供关于人类融合蛋白序列和3D结构的全面数据.
- 促进针对融合蛋白的向治疗策略的开发.
主要方法:
- 开发一个用于识别和分析融合蛋白的计算管道.
- 创建了FusionPDB,这是一个对人类融合蛋白序列和3D结构的精心策划的数据库.
- 蛋白质结构预测,质量评估 (pLDDT分数) 和虚拟查数据的整合.
主要成果:
- 融合PDB包含超过43,000个融合蛋白序列,包括14700个框架内融合基因.
- 该数据库包括超过3,500个独特的融合蛋白3D结构.
- 对于精选的融合蛋白质,提供了pLDDT评分分析和虚拟查结果.
结论:
- FusionPDB是一个独特的资源,提供完整的3D结构和关于人类融合蛋白的全面数据.
- 该资源解决了关键的知识差距,使得针对性治疗的进一步研究和开发成为可能.
- FusionPDB将不断更新,以涵盖所有人类融合蛋白.
相关概念视频
Tagging and Fusion Proteins
6.7K
Proteins are involved in several cellular processes and biochemical reactions. Analyzing a specific protein of interest requires it to be isolated from the other proteins in the cell. This is achieved by overexpressing the specific gene in a suitable host to produce large quantities of the target protein. A tag or label is recombined with the gene to produce a fusion protein containing the target protein and the tag. The tags on these fusion proteins can then be used for easy detection and...
6.7K
Gene Families
8.8K
Gene families consist of groups of genes proposed to have originated from a common ancestor. Typically these arise through events in which a gene or genes are mistakenly duplicated during cell division. Unlike their parent genes (which are subject to selection pressure to maintain function), these gene copies do not need to preserve their sequences and may evolve at a relatively faster rate.
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...
8.8K
Protein Families
15.4K
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...
15.4K
Globular and Fibrous Proteins
43.8K
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...
43.8K
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
Protein-protein Interfaces
12.5K
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...
12.5K


