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Search for "linear code" in Full Text gives 5 result(s) in Beilstein Journal of Organic Chemistry.
Monitoring carbohydrate 3D structure quality with the Privateer database
Beilstein J. Org. Chem. 2024, 20, 931–939, doi:10.3762/bjoc.20.83
- further inspection [16]. In addition to the SNFG, also displayed for each table entry is a copyable WURCS link, which encodes the complete glycan format in a linear code. The decision to present this information as a copyable link, as opposed to as plaintext is due to the inherent difficulty and
Introduction of a human- and keyboard-friendly N-glycan nomenclature
Beilstein J. Org. Chem. 2024, 20, 607–620, doi:10.3762/bjoc.20.53
- ) (Figure 5). Another difficulty is posed by the blood group H α1,2-fucose, which is linked to galactose, which in turn can be linked β1,3- or β1,4 to GlcNAc. So just putting “F” as the terminal sugar would leave uncertainty. Therefore – using linear code [41] – we write F2-A4. We – again – can save one
- “HNK-1” (from human natural killer cells) with sulfated glucuronic acid [47]. Annotating a structure like this requires some form of linear code and the addition of abbreviations for non-sugar substituents, in this case sulfate. Note that the hyphen binds the “su” to “Ga”, which in turn is hyphenated
GlycoBioinformatics
Beilstein J. Org. Chem. 2021, 17, 2726–2728, doi:10.3762/bjoc.17.184
- al. [7], wherein glycan substrate specificities and glycoenzyme reaction rules are described using an improved linear code that is standardized for use in analytical computational tools. This links with McDonald and Davey’s paper [8], which expands on their previously described theoretically derived
Simulating the enzymes of ganglioside biosynthesis with Glycologue
Beilstein J. Org. Chem. 2021, 17, 739–748, doi:10.3762/bjoc.17.64
- ], Tellurium [39], or other modelling software supporting this format. Glycan structures can be imported or exported as GlycoCT [40], and exported as Linear Code [41] or IUPAC condensed linear formats. Sets of structures can be downloaded as CSV or GlycoCT. A key function of Glycologue is the ability to
- structure identifiers can be exported as Linear Code, future support for the recently introduced LiCoRR (Linear Code for Reaction Rules) formalism [54] is also possible. Glycologue can incorporate the Neu5Gc and KDN variants of sialic acid, and predict structures containing these residues. However, they
A consensus-based and readable extension of Linear Code for Reaction Rules (LiCoRR)
Beilstein J. Org. Chem. 2020, 16, 2645–2662, doi:10.3762/bjoc.16.215
- clear glycan representation accessible to both computers and humans. Linear Code, a linearized and readily parsable glycan structure representation, is such a language. For this reason, Linear Code was adapted to represent reaction rules, but the syntax has drifted from its original description to
- accommodate new and originally unforeseen challenges. Here, we delineate the consensuses and inconsistencies that have arisen through this adaptation. We recommend options for a consensus-based extension of Linear Code that can be used for reaction rule specification going forward. Through this extension and
- specification of Linear Code to reaction rules, we aim to minimize inconsistent symbology thereby making glycan database queries easier. With a clear guide for generating reaction rule descriptions, glycan synthesis models will be more interoperable and reproducible thereby moving glycoinformatics closer to
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