桥梁世界:通过通用输入和规范化的命名体系,将甘氨酸表示与甘氨酸信息学连接起来
James Urban1,2, Roman Joeres1,2,3,4, Daniel Bojar1,2
1Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg 40530, Sweden.
Bioinformatics advances
|December 16, 2025
概括
一个新的通用输入框架自动化了糖甘命名体系的转换. 该工具通过标准化表示方式整合了多种不同的甘氨酸数据库和计算工具,增强了甘氨酸生物学的数据共享.
科学领域:
- 葡萄糖科学 (Glycoscience) 是一种科学.
- 计算生物学 计算生物学
- 生物信息学是一种生物信息学.
背景情况:
- 葡萄糖生物学领域使用了各种不同的命名系统来命名葡萄糖.
- 这种多重的甘氨酸命名系统对数据集成和知识共享提出了挑战.
研究的目的:
- 开发一个用于自动化转换甘氨酸命名体系的实用框架.
- 为了提高可用性和数据集成,将甘氨酸表示标准化.
主要方法:
- 实现了一个通用输入框架,能够处理多个甘氨酸命名系统.
- 开发了一种自动化转换过程,将其转换为规范化的IUPAC缩缩格式.
- 处理了常见的命名,字体错误,结构模两可,以及复杂的甘氨酸特征.
主要成果:
- 通用输入框架成功地将超过10种命名体系转化为标准化格式.
- 在超过15万个序列上实现了高覆盖率 (98%-100%) 和速度 (每甘氨酸<1毫秒).
- 证明了现有的甘氨酸数据库和工具的无集成.
结论:
- 通用输入框架增强了糖生物学中的数据互操作性.
- 这种工具有助于在不同的甘氨酸表示系统中进行知识共享和计算分析.
- 该框架以glycowork Python包和Web应用程序的形式提供.
相关概念视频
Protein Glycosylation
9.2K
Glycosylation, the most common post-translational modification for proteins, serves diverse functions. Adding sugars to proteins makes the proteins more resistant to proteolytic digestion. Glycosylated proteins can act as markers and receptors to promote cell-cell adhesion. Additionally, they have many essential quality control functions in the cell, such as correct protein folding and facilitating transport of misfolded proteins to the cytosol, which can be degraded.
Glycosylation occurs in...
Glycosylation occurs in...
9.2K
Oligosaccharide Assembly
3.5K
Protein glycosylation starts in the ER lumen and continues in the Golgi apparatus. Glycosyltransferases catalyze the addition of sugar molecules or glycosylation of proteins. Usually, these enzymes add sugars to the hydroxyl groups of selected serine or threonine residues to form O-linked glycans or the amino groups of asparagine residues to form N-linked glycans. Different positions on the same polypeptide chain can contain differently linked glycans.
Multiple sugar molecules that may or may...
Multiple sugar molecules that may or may...
3.5K
Proteoglycans
4.6K
Glycans, a class of complex heterogeneous molecules, can be covalently attached to proteins to form glycosylated proteins that regulate various physiological and pathological processes. Glycosylated proteins or glycoproteins comprise N-linked and O-linked oligosaccharides. O-glycosylation is the most common type of protein glycosylation. Here, glycans attach to the oxygen atom of the hydroxyl groups of Serine or Threonine residues. O-linked glycosylation occurs later in protein processing,...
4.6K
Glycocalyx and its Functions
7.7K
The glycocalyx is a carbohydrate-rich, fuzzy-appearing layer on the outer surface of the cell membrane. It is highly hydrophilic, because of this it attracts large amounts of water to the cell's surface. This aids the cell's interaction with the watery environment and also helps it to obtain substances dissolved in the water. It is also important for cell identification, self/non-self determination, and embryonic development and is used in cell-to-cell attachments to form tissues.
7.7K
Molecular Compounds: Formulas and Nomenclature
54.9K
Molecular compounds or covalent compounds result when atoms share electrons to form covalent bonds. Since there is no electron transfer, molecular compounds do not contain ions; instead, they consist of discrete, neutral molecules.
54.9K
IUPAC Nomenclature of Carboxylic Acids
12.0K
IUPAC names of carboxylic acids are systematically derived following a few rules discussed below.
For acyclic saturated monocarboxylic acids, the longest hydrocarbon chain containing the –COOH carbon is identified as the parent chain. Then, the last -e of the parent hydrocarbon name is replaced with a suffix -oic acid.
For acyclic saturated monocarboxylic acids, the longest hydrocarbon chain containing the –COOH carbon is identified as the parent chain. Then, the last -e of the parent hydrocarbon name is replaced with a suffix -oic acid.
12.0K


