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Search for "glycoinformatics" in Full Text gives 9 result(s) in Beilstein Journal of Organic Chemistry.
GlycoBioinformatics
Beilstein J. Org. Chem. 2021, 17, 2726–2728, doi:10.3762/bjoc.17.184
- , Queensland 4222, Australia Department of Molecular Sciences, Macquarie University, Sydney, New South Wales, Australia 10.3762/bjoc.17.184 Keywords: bioinformatics; glycobioinformatics; glycoinformatics; In order to introduce this thematic issue “GlycoBioinformatics” [1] in the Beilstein Journal of Organic
A systems-based framework to computationally describe putative transcription factors and signaling pathways regulating glycan biosynthesis
Beilstein J. Org. Chem. 2021, 17, 1712–1724, doi:10.3762/bjoc.17.119
- relationships, the starting point for experimental system-wide validation. Keywords: ChIP-Seq; glycoinformatics; glycosylation; TCGA transcription factor; Introduction The glycan signatures of cells and tissue are controlled by the expression pattern of 300–350 glycosylating-related genes that are together
- signaling pathways contribute to altered glycan structures in diseases such as diabetes and cancer. Thus, this work represents a rich starting point for wet-lab validation and glycoinformatics DB construction. Visualizing TF–glycogene interaction networks revealed communities of glycogenes in each cancer
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
- 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
- compliance with FAIR standards. Here, we present Linear Code for Reaction Rules (LiCoRR), version 1.0, an unambiguous representation for describing glycosylation reactions in both literature and code. Keywords: glycoinformatics; linear code; systems glycobiology; Introduction Glycans are predominantly
- tackle increasingly complex glycan synthesis problems owing to the advent of a number of enabling computational modeling technologies. Linear Code is used to represent reaction rules of glycan synthesis thereby bringing both human-readability and computer-parsability to the glycoinformatics space. The
Comparative ligand structural analytics illustrated on variably glycosylated MUC1 antigen–antibody binding
Beilstein J. Org. Chem. 2020, 16, 2540–2550, doi:10.3762/bjoc.16.206
- ]. Originally built to support bioinformatics, Galaxy now supports a much more expansive community including proteomics [2], metabolomics [3], cheminformatics [4], glycoinformatics [5], and chemistry [6]. Of value to these communities are the broad range of tools and ways to connect tools (workflows) in Galaxy
Leveraging glycomics data in glycoprotein 3D structure validation with Privateer
Beilstein J. Org. Chem. 2020, 16, 2523–2533, doi:10.3762/bjoc.16.204
- the validation of 3D glycoprotein structures. Keywords: electron cryomicroscopy; glycoinformatics; glycomics; Privateer; X-ray crystallography; Introduction Glycosylation-related processes are prevalent in life. The attachment of carbohydrates to macromolecules extends the capabilities of cells to
Computational tools for drawing, building and displaying carbohydrates: a visual guide
Beilstein J. Org. Chem. 2020, 16, 2448–2468, doi:10.3762/bjoc.16.199
- this tool ideal for integrated use with various glycoinformatics software and also for applications in glycoproteomics, glycomics and mass spectrometry (MS). One of the illustrations involves combined use with the gpAnnotate application, dedicated to score and annotate MS/MS glycopeptide spectrums in
Tools for generating and analyzing glycan microarray data
Beilstein J. Org. Chem. 2020, 16, 2260–2271, doi:10.3762/bjoc.16.187
- growing resource for the inclusion of data from multiple sources for glycoinformatics [41]. A component of the project involves the creation of a glycan microarray data repository, whereby anyone can go to a website and deposit and view glycan microarray data, along with the metadata associated with the
How and why plants and human N-glycans are different: Insight from molecular dynamics into the “glycoblocks” architecture of complex carbohydrates
Beilstein J. Org. Chem. 2020, 16, 2046–2056, doi:10.3762/bjoc.16.171
- micro- (or macro-)heterogeneity of glycan sequences at specific sites [7]. These complexities are very difficult to resolve, requiring high levels of expertise and multi-layered orthogonal approaches [7][8][9][10]. Within this framework, the contribution of glycoinformatics tools and databases
The use of glycoinformatics in glycochemistry
Beilstein J. Org. Chem. 2012, 8, 915–929, doi:10.3762/bjoc.8.104
- Thomas Lutteke Justus-Liebig-University Gießen, Institute of Veterinary Physiology and Biochemistry, Frankfurter Str. 100, 35392 Gießen, Germany 10.3762/bjoc.8.104 Abstract Glycoinformatics is a small but growing branch of bioinformatics and chemoinformatics. Various resources are now available
- aid with quality control. Specific problems of glycoinformatics compared to bioinformatics for genomics or proteomics, especially concerning integration and long-term maintenance of the existing glycan databases, are also discussed. Keywords: carbohydrates; databases; glycomics; software
- ]. Furthermore, there are much less primary data on carbohydrates available than, e.g., on proteins, to test or train the algorithms [8]. For these reasons, glycoinformatics as a research area at the intersection of bioinformatics and chemoinformatics has been considered to be lagging behind its sister fields
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