GlycoMinestruct: A new bioinformatics tool for highly accurate mapping of the human N-linked and O-linked glycoproteomes by incorporating structural features

Fuyi Li, Chen Li, Jerico Revote, Yang Zhang, Geoffrey I. Webb, Jian Li, Jiangning Song, Trevor Lithgow

Research output: Contribution to journalArticleResearchpeer-review

25 Citations (Scopus)

Abstract

Glycosylation plays an important role in cell-cell adhesion, ligand-binding and subcellular recognition. Current approaches for predicting protein glycosylation are primarily based on sequence-derived features, while little work has been done to systematically assess the importance of structural features to glycosylation prediction. Here, we propose a novel bioinformatics method called GlycoMinestruct (http://glycomine.erc.monash.edu/Lab/GlycoMine-Struct/) for improved prediction of human N- and O-linked glycosylation sites by combining sequence and structural features in an integrated computational framework with a two-step feature-selection strategy. Experiments indicated that GlycoMinestruct outperformed NGlycPred, the only predictor that incorporated both sequence and structure features, achieving AUC values of 0.941 and 0.922 for N- and O-linked glycosylation, respectively, on an independent test dataset. We applied GlycoMinestruct to screen the human structural proteome and obtained high-confidence predictions for N- and O-linked glycosylation sites. GlycoMinestruct can be used as a powerful tool to expedite the discovery of glycosylation events and substrates to facilitate hypothesis-driven experimental studies.

Original languageEnglish
Article number34595
Number of pages16
JournalScientific Reports
Volume6
DOIs
Publication statusPublished - 6 Oct 2016

Keywords

  • glycosylation
  • protein structure predictions

Cite this