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J Chem Inf Model. 2017 Apr 24;57(4):632-637. doi: 10.1021/acs.jcim.6b00650. Epub 2017 Mar 22.

WURCS 2.0 Update To Encapsulate Ambiguous Carbohydrate Structures.

Author information

1
The Noguchi Institute , Itabashi, Tokyo 173-0003, Japan.
2
Faculty of Science and Engineering, Soka University , Hachioji, Tokyo 192-8577, Japan.
3
Glycoscience and Glycotechnology Research Group, Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST) , Tsukuba, Ibaraki 305-8568, Japan.

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.

PMID:
28263066
DOI:
10.1021/acs.jcim.6b00650
[Indexed for MEDLINE]
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