LINUCS: LInear Notation for Unique description of Carbohydrate Sequences

Bohne-Lang, Andreas; Lang, Elke; Förster, Thomas; Lieth, Claus-W. von der

doi:10.1016/s0008-6215(01)00230-0

Cited by 116 publications

(52 citation statements)

References 14 publications

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“…Structural data can be imported into the drawing panel from various encoding formats in use by existing databases initiatives, such as: LINUCS 26 used by the Glycosciences.de 27 portal, the format devised by GlycoMinds Ltd 28 used by the Consortium for Functional Glycomics 29 and Glyco-CT 30 developed by the EUROCarbDB initiative 17 . In this way structures that are already defined and stored in a database can be easily tested against the acquired spectra.…”

Section: Input and Display Of Structuresmentioning

confidence: 99%

GlycoWorkbench: A Tool for the Computer-Assisted Annotation of Mass Spectra of Glycans

et al. 2008

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Mass spectrometry is the main analytical technique currently used to address the challenges of glycomics as it offers unrivalled levels of sensitivity and the ability to handle complex mixtures of different glycan variations. Determination of glycan structures from analysis of MS data is a major bottleneck in high-throughput glycomics projects, and robust solutions to this problem are of critical importance. However, all the approaches currently available have inherent restrictions to the type of glycans they can identify and none of them has proved to be a definitive tool for glycomics.GlycoWorkbench is a software tool developed by the EUROCarbDB initiative to assist the manual interpretation of MS data. The main task of GlycoWorkbench is to evaluate a set of structures proposed by the user by matching the corresponding theoretical list of fragment masses against the list of peaks derived from the spectrum. The tool provides an easy to use graphical interface, a comprehensive and increasing set of structural constituents, an exhaustive collection of fragmentation types, and a broad list of annotation options. The aim of GlycoWorkbench is to offer complete support for the routine interpretation of MS data. The software is available for download from: http://www.eurocarbdb.org/applications/ms-tools.

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Section: Input and Display Of Structuresmentioning

confidence: 99%

GlycoWorkbench: A Tool for the Computer-Assisted Annotation of Mass Spectra of Glycans

et al. 2008

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“…Statistical analysis of glycosylation sites in the PDB and SwissProt http://www.glycosciences.de/tools/glyseq/ [61] 46 GlyVicinity Statistical analysis of protein-carbohydrate interactions data from the PDB http://www.glycosciences.de/tools/ glyvicinity/ [61] 3D structure/conformation tools 47 Sweet-II Generation of carbohydrate 3D structure models http://www.glycosciences.de/modeling/ sweet2/ [62] 48 Glycam Biomolecule Builder Generation of carbohydrate 3D structure models http://www.glycam.com/CCRC/biombuilder/ biomb_index.jsp [63] 49 pdb2linucs Detection of carbohydrate moieties in PDB structures http://www.glycosciences.de/tools/ pdb2 linucs/ [23] 50 pdb-care Validation of carbohydrate 3D structures http://www.glycosciences.de/tools/pdb-care/ [64] 51 CARP Carbohydrate Ramachandran Plot http://www.glycosciences.de/tools/carp/ [61] 52 GlyTorsion Statistical analysis of torsion angles derived from the PDB http://www.glycosciences.de/tools/ glytorsion/ [61] 53 GlyProt In silico glycosylation of proteins http://www.glycosciences.de/modeling/ glyprot/ [65] 54 Dynamic Molecules Online molecular dynamics (MD) simulations http://www.md-simulations.de [66] Notation and graphical representation of carbohydrates 55 IUPAC Official IUPAC recommendations for carbohydrate notation http://www.chem.qmul.ac.uk/iupac/2carb/ [67] 56 LINUCS Linear notation for carbohydrate structures http://www.glycosciences.de/tools/linucs/ [68] 57 LiGraph Graphical representation of carbohydrate structures http://www.glycosciences.de/tools/LiGraph/ [14] 58 KEGG CSM Composite Structure Map, graphical query tool for KEGG databases http://www.genome.jp/kegg-bin/draw_csm [69] 59 Glycan Builder Graphical input of carbohydrate structures http://www.eurocarbdb.org/applications/ structure-tools/ [70] www.chembiochem.org ously query the BCSDB and the GLYCO-SCIENCES.de databases [18] and to crosslink structures of the CFG and the GLY-COSCIENCES.de databases. Therefore, users who are exploring an entry in one of these two databases, for which there is also information in the other database, can easily access all of the data in both resources.…”

Section: Cbs Prediction a C H T U N G T R E N N U N G Servers Predictmentioning

confidence: 99%

Web Resources for the Glycoscientist

Lütteke

2008

ChemBioChem

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“…Subsequent initiatives using relational databases opted for storing the carbohydrate sequences as linear strings, similar to those used in protein or nucleotide databases. These strings were generated through an ordered traversal of the carbohydrate sequences and could thus serve as primary keys in database systems (e.g., string representations such as those used in LINUCS, 4 GlycoSuiteDB, 5,6 LinearCode 7 and the bacterial carbohydrate structure database (BCSDB) encoding 8 ). Later the connectivity information in carbohydrate sequences was stored using connection tablelike representations (KCF 9 ).…”

Section: Introductionmentioning

confidence: 99%