New Features of Carbohydrate Structure Database Notation (CSDB Linear), As Compared to Other Carbohydrate Notations

The CSDB Linear notation for carbohydrate sequences utilized in the Carbohydrate Structure Database (CSDB) has been improved to meet modern requirements in glycoinformatics. The new features include: the possibility to combine repeating and nonrepeating moieties in one structure; support of carbon–c...

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Bibliographic Details
Published inJournal of chemical information and modeling Vol. 60; no. 3; pp. 1276 - 1289
Main Authors Toukach, Philip V, Egorova, Ksenia S
Format Journal Article
LanguageEnglish
Published United States American Chemical Society 23.03.2020
Subjects
Carbohydrates
Carbon
Covalent bonds
Error detection
Glycan
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Summary:The CSDB Linear notation for carbohydrate sequences utilized in the Carbohydrate Structure Database (CSDB) has been improved to meet modern requirements in glycoinformatics. The new features include: the possibility to combine repeating and nonrepeating moieties in one structure; support of carbon–carbon bonds; and usage of SMILES encodings for unambiguous chemical description of glycan structures, including aglycons and atypical components. The new capabilities of CSDB Linear, together with the older ones, allow efficient detection of errors in CSDB and, at the same time, ensure the absence of informatic problems common for human-readable notations. The CSDB Linear implementation provides translation to other carbohydrate notations and multiple procedures for content error checking.
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ISSN:1549-9596
1549-960X
DOI:10.1021/acs.jcim.9b00744