W3-SWEET: Carbohydrate Modeling By Internet

Böhne, Andreas; Lang, Elke; Lieth, Claus‐Wilhelm von der

doi:10.1007/s008940050068

Cited by 73 publications

(48 citation statements)

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“…The user can

select the type of N -glycan (e.g. oligomannose rich, complex, hybrid, very large); by default a typical structure for each class is taken;

select an N -glycan from a database of >1000 structures (Figure 4) constructed using SWEET-II (11) and optimized using the TINKER MM3 force field (); the database is searchable by N -glycan composition;construct the desired N -glycan using SWEET-II by user input of the desired structure using the extended IUPAC nomenclature. If the coordinates provided already contain attached N -glycans, the user can either accept this orientation or use the procedure described above to align the glycan moiety.…”

Section: Methodsmentioning

confidence: 99%

GlyProt: in silico glycosylation of proteins

Bohne-Lang

Lieth

2005

Nucleic Acids Research

203

156

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GlyProt () is a web-based tool that enables meaningful N-glycan conformations to be attached to all the spatially accessible potential N-glycosylation sites of a known three-dimensional (3D) protein structure. The probabilities of physicochemical properties such as mass, accessible surface and radius of gyration are calculated. The purpose of this service is to provide rapid access to reliable 3D models of glycoproteins, which can subsequently be refined by using more elaborate simulations and validated by comparing the generated models with experimental data.

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“…The user can

select the type of N -glycan (e.g. oligomannose rich, complex, hybrid, very large); by default a typical structure for each class is taken;

Section: Methodsmentioning

confidence: 99%

GlyProt: in silico glycosylation of proteins

Bohne-Lang

Lieth

2005

Nucleic Acids Research

203

156

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“…13) "GlycoFragment" enables the easy generation of all theoretically possible A-, B-, C-, X-, Y-and Z-fragments of a de ned glycan structure according to the de nitions of Domon and Costello. 14) e algorithm uses the Sweet-II 15,16) program to interpret nomenclature and chooses suitable templates from a database according to linkage information. "GlycoSearchMS" imports a mass spectrum to a database search of theoretically calculated spectra and identi es the best candidate spectra.…”

Section: Ms Approaches For Released Glycan Analysismentioning

confidence: 99%

A Brief Review of Bioinformatics Tools for Glycosylation Analysis by Mass Spectrometry

Tsai

Chen

2017

Mass Spectrometry

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e purpose of this review is to provide updated information regarding bioinformatic so ware for the use in the characterization of glycosylated structures since 2013. A comprehensive review by Woodin et al. Analyst 138: 2793Analyst 138: -2803Analyst 138: , 2013 described two main approaches that are introduced for starting researchers in this area; analysis of released glycans and the identi cation of glycopeptide in enzymatic digests, respectively. Complementary to that report, this review focuses on mass spectrometry related bioinformatics tools for the characterization of N-linked and O-linked glycopeptides. Speci cally, it also provides information regarding automated tools that can be used for glycan pro ling using mass spectrometry.

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“…The initial three-dimensional model of GT1b-OS was constructed with the SWEET software (40) and superimposed on the GT1b-␤A structure using LSQKAB (41). The fit was improved with cycles of manual adjustment to the glycosidic torsion angles of the GT1b-OS (QUANTA) followed by superposition with LSQKAB.…”

Section: Structure Of Tent Hc-ganglioside Complexmentioning

confidence: 99%