Since 1971, the Protein Data Bank (PDB) has served as the single global archive for experimentally determined 3D structures of biological macromolecules made freely available to the global community according to the FAIR principles of Findability–Accessibility–Interoperability–Reusability. During the first 50 years of continuous PDB operations, standards for data representation have evolved to better represent rich and complex biological phenomena. Carbohydrate molecules present in more than 14,000 PDB structures have recently been reviewed and remediated to conform to a new standardized format. This machine-readable data representation for carbohydrates occurring in the PDB structures and the corresponding reference data improves the findability, accessibility, interoperability and reusability of structural information pertaining to these molecules. The PDB Exchange MacroMolecular Crystallographic Information File data dictionary now supports (i) standardized atom nomenclature that conforms to International Union of Pure and Applied Chemistry-International Union of Biochemistry and Molecular Biology (IUPAC-IUBMB) recommendations for carbohydrates, (ii) uniform representation of branched entities for oligosaccharides, (iii) commonly used linear descriptors of carbohydrates developed by the glycoscience community and (iv) annotation of glycosylation sites in proteins. For the first time, carbohydrates in PDB structures are consistently represented as collections of standardized monosaccharides, which precisely describe oligosaccharide structures and enable improved carbohydrate visualization, structure validation, robust quantitative and qualitative analyses, search for dendritic structures and classification. The uniform representation of carbohydrate molecules in the PDB described herein will facilitate broader usage of the resource by the glycoscience community and researchers studying glycoproteins.

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蛋白质数据库中碳水化合物分子的现代化统一表示

自 1971 年以来，蛋白质数据库 (PDB) 一直是通过实验确定的生物大分子 3D 结构的单一全球档案，根据可查找性、可访问性、互操作性、可重用性的 FAIR 原则免费向全球社区免费提供。在 PDB 连续运行的前 50 年中，数据表示标准不断发展，以更好地表示丰富而复杂的生物现象。最近对超过 14,000 个 PDB 结构中存在的碳水化合物分子进行了审查和修复，以符合新的标准化格式。这种 PDB 结构中碳水化合物的机器可读数据表示和相应的参考数据提高了与这些分子相关的结构信息的可查找性、可访问性、互操作性和可重用性。PDB Exchange 宏观分子晶体信息文件数据字典现在支持 (i) 符合国际纯粹与应用化学联合会 - 国际生物化学和分子生物学联合会 (IUPAC-IUBMB) 关于碳水化合物的建议的标准化原子命名法，(ii) 碳水化合物的统一表示法寡糖的分支实体，(iii) 糖科学界开发的碳水化合物的常用线性描述符，以及 (iv) 蛋白质中糖基化位点的注释。PDB 结构中的碳水化合物首次一致地表示为标准化单糖的集合，它精确地描述了寡糖结构，并能够改进碳水化合物的可视化、结构验证、稳健的定量和定性分析、搜索树突结构和分类。本文描述的 PDB 中碳水化合物分子的统一表示将有助于糖科学界和研究糖蛋白的研究人员更广泛地使用该资源。