WURCS 2.0 Update To Encapsulate Ambiguous Carbohydrate Structures
WURCS 2.0 Update To Encapsulate Ambiguous Carbohydrate Structures
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DOI：
10.1021/acs.jcim.6b00650
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发表时间：
2017-04-01
影响因子：
5.6
通讯作者：
Narimatsu, Hisashi
中科院分区：
文献类型：
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作者：
Matsubara, Masaaki;Aoki-Kinoshita, Kiyoko F.;Narimatsu, Hisashi
结构模糊性的准确表示对于在文献和数据库中存储含有不同程度的模糊性的碳水化合物结构是重要的。虽然过去已经开发了许多碳水化合物的表示，但不存在通用但离散的表示格式。我们以前开发了Web3碳水化合物结构的唯一表示法（WURCS），试图为碳水化合物结构定义一个可推广的和唯一的线性表示法。然而，它缺乏足够的规则来唯一地描述模糊的结构。在这项工作中，我们更新了WURCS来处理这种模糊的单糖结构。特别是，处理周围（潜在的）羰基结构的模糊性附带的碳水化合物分析，我们定义了一个代表性的骨架碳原子水平的模糊性。因此，我们表明，WURCS 2.0可以代表更广泛的各种碳水化合物结构，含有模棱两可的单糖，如那些闭环是未定义的或其异头信息是唯一已知的。这种新格式提供了以前不可能的碳水化合物的表示，目前正在由国际聚糖结构库GlyTouCan使用。
Accurate representation of structural ambiguity is important for storing carbohydrate structures containing varying levels of ambiguity in the literature and databases. Although many representations for carbohydrates have been developed in the past, a generalized but discrete representation format did not exist. We had previously developed the Web3 Unique Representation of Carbohydrate Structures (WURCS) in an attempt to define a generalizable and unique linear representation for carbohydrate structures. However, it lacked sufficient rules to uniquely describe ambiguous structures. In this work, we updated WURCS to handle such ambiguous monosaccharide structures. In particular, to handle structural ambiguity around (potential) carbonyl groups incidental to the carbohydrate analysis, we defined a representation of backbone carbons containing atomic-level ambiguity. As a result, we show that WURCS 2.0 can represent a wider variety of carbohydrate structures containing ambiguous monosaccharides, such as those whose ring closure is undefined or whose anomeric information is only known. This new format provides a representation of carbohydrates that was not possible before, and it is currently being used by the International Glycan Structure Repository GlyTouCan.