WURCS 2.0 Update To Encapsulate Ambiguous Carbohydrate Structures.

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ID: 275435
2017
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Abstract
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.
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matsubara2017wurcsjournal Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors Matsubara, Masaaki;Aoki-Kinoshita, Kiyoko F;Aoki, Nobuyuki P;Yamada, Issaku;Narimatsu, Hisashi;
Journal Journal of chemical information and modeling
Year 2017
DOI
10.1021/acs.jcim.6b00650
URL
Keywords
glycan sequence format glycan visualization glyco bioinformatics sequence conversion symbolic notation

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