Databases and Bioinformatic Tools for Glycobiology and Glycoproteomics

Abstract

Glycosylation plays critical roles in various biological processes and is closely related to diseases. Deciphering the glycocode in diverse cells and tissues offers opportunities to develop new disease biomarkers and more effective recombinant therapeutics. In the past few decades, with the development of glycobiology, glycomics, and glycoproteomics technologies, a large amount of glycoscience data has been generated. Subsequently, a number of glycobiology databases covering glycan structure, the glycosylation sites, the protein scaffolds, and related glycogenes have been developed to store, analyze, and integrate these data. However, these databases and tools are not well known or widely used by the public, including clinicians and other researchers who are not in the field of glycobiology, but are interested in glycoproteins. In this study, the representative databases of glycan structure, glycoprotein, glycan–protein interactions, glycogenes, and the newly developed bioinformatic tools and integrated portal for glycoproteomics are reviewed. We hope this overview could assist readers in searching for information on glycoproteins of interest, and promote further clinical application of glycobiology.

The Hitchhiker's guide to glycoproteomics

“…A suite of computational tools has been developed over the past decade, which have strongly contributed to the maturation and application of glycoproteomics (Table 2). While these informatics solutions have made impressive progress as summarised in recent reviews [39,103,170,[172][173][174], some challenges remain. A recent inter-laboratory study conducted by the HUPO human glycoproteome initiative (HGI) to evaluate the performance of current software solutions and to identify high-performance search strategies for glycoproteomics data analysis, identified several high-performance software solutions, and at the same time demonstrated the significant informatics challenges that remain for glycopeptide data analysesan important step forward to improve glycoproteomics software performance [171].…”

Prospects and Challenges of the Study of Anti-Glycan Antibodies and Microbiota for the Monitoring of Gastrointestinal Cancer

“…In recent years, various glycomic databases and tools have been generated [135]. Databases are available on glycan-binding proteins and glycan-mediated host-pathogen interactions.…”

Insights into Bioinformatic Applications for Glycosylation: Instigating an Awakening towards Applying Glycoinformatic Resources for Cancer Diagnosis and Therapy

“…Bioinformatic resources have become popular in glycan research for automation of analytical outputs and for high throughput processing of data. The analysis of glycans is challenging, this is Bioinformatics resources for glycomics and glycobiology-related databases has been reviewed [28][29][30][31][32][33][34]. The application of bioinformatic tools in biology has led to a fundamental understanding of the biological processes involved [35,36].…”

“…The hallmarks of glycosylation in cancer are presented in Figure 2. Bioinformatics resources for glycomics and glycobiology-related databases has been reviewed [28][29][30][31][32][33][34]. The application of bioinformatic tools in biology has led to a fundamental understanding of the biological processes involved [35,36].…”