title: GlycoMinestruct: a new bioinformatics tool for highly accurate mapping of the human N-linked and O-linked glycoproteomes by incorporating structural features.
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 GlycoMinestructoutperformed 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 GlycoMinestructto screen the human structural proteome and obtained high-confidence predictions for N- and O-linked glycosylation sites. GlycoMinestructcan be used as a powerful tool to expedite the discovery of glycosylation events and substrates to facilitate hypothesis-driven experimental studies.
authors.affiliation: College of Information Engineering, Northwest A&F University, Yangling 712100, China.|Infection and Immunity Program, Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia.
authors.forename: Fuyi
authors.initials: F
authors.lastname: Li
authors.affiliation: Infection and Immunity Program, Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia.
authors.forename: Chen
authors.initials: C
authors.lastname: Li
authors.affiliation: Monash Bioinformatics Platform, Monash University, Melbourne, VIC 3800, Australia.
authors.forename: Jerico
authors.initials: J
authors.lastname: Revote
authors.affiliation: College of Information Engineering, Northwest A&F University, Yangling 712100, China.
authors.forename: Yang
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: Monash Centre for Data Science, Faculty of Information Technology, Monash University, Melbourne, VIC 3800, Australia.
authors.forename: Geoffrey I
authors.initials: GI
authors.lastname: Webb
authors.affiliation: Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, VIC 3800, Australia.
authors.forename: Jian
authors.initials: J
authors.lastname: Li
authors.affiliation: Infection and Immunity Program, Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia.|Monash Centre for Data Science, Faculty of Information Technology, Monash University, Melbourne, VIC 3800, Australia.|National Engineering Laboratory for Industrial Enzymes and Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.
authors.forename: Jiangning
authors.initials: J
authors.lastname: Song
authors.affiliation: Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, VIC 3800, Australia.
authors.forename: Trevor
authors.initials: T
authors.lastname: Lithgow
mesh_terms: D019295:Computational Biology; D006023:Glycoproteins / Q000737:chemistry / Q000235:genetics; D006031:Glycosylation; D006801:Humans; D020543:Proteome / Q000737:chemistry / Q000235:genetics; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software
chemical_list: D006023:Glycoproteins; D020543:Proteome