Cited by 175Glycosylation and Glycoproteins ResearchMachine Learning in Bioinformaticsvaccines and immunoinformatics approaches

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NetCGlyc 1.0: prediction of mammalian C-mannosylation sites

Julenius, Karin·2007·Glycobiology

DOI 10.1093/glycob/cwm050

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Abstract

C-mannosylation is the attachment of an alpha-mannopyranose to a tryptophan via a C-C linkage. The sequence WXXW, in which the first Trp becomes mannosylated, has been suggested as a consensus motif for the modification, but only two-thirds of known sites follow this rule. We have gathered a data set of 69 experimentally verified C-mannosylation sites from the literature. We analyzed these for sequence context and found that apart from Trp in position +3, Cys is accepted in the same position. We also find a clear preference in position +1, where a small and/or polar residue (Ser, Ala, Gly, and Thr) is preferred and a Phe or a Leu residue discriminated against. The Protein Data Bank was searched for structural information, and five structures of C-mannosylated proteins were obtained. We showed that modified tryptophan residues are at least partly solvent exposed. A method predicting the location of C-mannosylation sites in proteins was developed using a neural network approach. The best overall network used a 21-residue sequence input window and information on the presence/absence of the WXXW motif. NetCGlyc 1.0 correctly predicts 93% of both positive and negative C-mannosylation sites. This is a significant improvement over the WXXW consensus motif itself, which only identifies 67% of positive sites. NetCGlyc 1.0 is available at http://www.cbs.dtu.dk/services/NetCGlyc/. Using NetCGlyc 1.0, we scanned the human genome and found 2573 exported or transmembrane transcripts with at least one predicted C-mannosylation site.

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Authors: Julenius, K.
Affiliations: Stockholm University (SE)
Corresponding author: Julenius, Karin
Venue: Glycobiology
Publisher: Oxford University Press (OUP)
Published: 2007-05-09
Volume: 17
Issue: 8
Pages: 868-876
ISSN: 0959-6658 (ISSN-L)
1460-2423
DOI: 10.1093/glycob/cwm050
OpenAlex: W2152890174
Cited by: 174
References: 50
Citations by year: 2026: 5 · 2025: 7 · 2024: 11 · 2023: 3 · 2022: 8 · 2021: 11 · 2020: 15 · 2019: 8 · 2018: 11 · 2017: 15 · 2016: 15 · 2015: 6 · 2014: 14 · 2013: 8 · 2012: 9
FWCI: 2.65
Type: journal article
Language: en
Open access: closed
Locations: Glycobiology (publishedVersion)
PubMed (publishedVersion)
Funders: Knut och Alice Wallenbergs Stiftelse
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Glycosylation and Glycoproteins Research
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Machine Learning in Bioinformatics
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › vaccines and immunoinformatics approaches
Keywords: C-mannosylation, glycosylation site prediction, sequence context, solvent exposure, neural network classifier, mammalian proteins, human genome, transmembrane proteins
MeSH terms: Algorithms, Amino Acid Sequence, Animals, Glycoproteins, Humans, Mammals, Mannose, Models, Molecular, Molecular Sequence Data, Genome, Human, Neural Networks, Computer, Amino Acid Motifs, Databases, Protein

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NetCGlyc 1.0: prediction of mammalian C-mannosylation sites

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