ArticleNature methods2024
Restoring protein glycosylation with GlycoShape.
Article in Nature methods, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 51 papers.
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Who cites it
51 citing papers in PubMed.
- Site-specific O-glycans influence lacritin structure and multimerization in tears.Protein science : a publication of the Protein Society · 2026Article
- Post‑translational modification‑governed immune states in cancer immunity: Biomarker implications for checkpoint competence, tumor visibility and immunotherapy resistance (Review).International journal of oncology · 2026Review
- Structural basis of diverse antibody recognition of conserved coronavirus spike S2 epitopes that contribute to protective immunity.bioRxiv : the preprint server for biology · 2026Article
- Unraveling the Glycosylation Machinery ofInternational journal of molecular sciences · 2026Article
- Automating Model Building for SPM Images of Biomolecules Using MISO.Journal of chemical information and modeling · 2026Article
- Fucosyltransferases in asthma: regulators of epithelial dysfunction, senescence, and airway inflammation.Clinical reviews in allergy & immunology · 2026Review
- Glycosylation orchestrates megakaryocytic fate of hematopoietic stem cells via Wnt-MUC13 signaling.Nature communications · 2026Article
- Structure-based design of stable recombinant hepatitis C virus E1E2 heterodimers.Nature communications · 2026Article
- A Glycan-Aware Diffusion Model for Carbohydrate and Glycoprotein Structure Prediction.bioRxiv : the preprint server for biology · 2026Article
- Guidelines for Comparing Circular Dichroism Spectroscopy and Molecular Dynamics Simulations for Biomolecules.Chemphyschem : a European journal of chemical physics and physical chemistry · 2026Article
- Induction of broadly neutralizing HIV antibodies by a two-step mechanism informs vaccine design.Science (New York, N.Y.) · 2026Article
- Diverse germline-targeting HIV Env immunogens select for distinct mutations in the same knock-in mice B cell receptors.Nature communications · 2026Article
- The ligand preference of LRP1 is regulated by O-glycans.Science advances · 2026Article
- Advances and challenges in multiscale biomolecular simulations: artificial intelligence-driven paradigm shift.Quantitative biology (Beijing, China) · 2026Article
- Glycoprotein biosensor boosted by signal amplification of heparin polysaccharide and insights into glycan-lectin recognition.Mikrochimica acta · 2026Article
- Accelerating molecular dynamics simulations using fast Ewald summation with prolates.Nature communications · 2026Article
- Leveraging Glycan-Glycan Interactions to Tune the Conformation of Glycan Hairpins and Build Rigid 3D Architectures.Journal of the American Chemical Society · 2026Article
- O-Mannose Glycosylations Influence E-Cadherin Functional Interactions.Molecular & cellular proteomics : MCP · 2026Article
- Chemically Defined Non-human Glycans Comprising Galactose-α1-3-Galactose (α-Gal) Epitopes Glycoengineered into the Fragment Antigen-Binding (Fab) Domain of Cetuximab Differentially Affect Human Anti-α-Gal Immunoglobulin E (IgE) Binding.ACS pharmacology & translational science · 2026Article
- Site-specific O-glycans influence lacritin structure and multimerization in tears.bioRxiv : the preprint server for biology · 2026Article
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Authors and funding
8 authors.
Funding
Abstract
Despite ground-breaking innovations in experimental structural biology and protein structure prediction techniques, capturing the structure of the glycans that functionalize proteins remains a challenge. Here we introduce GlycoShape ( https://glycoshape.org ), an open-access glycan structure database and toolbox designed to restore glycoproteins to their native and functional form in seconds. The GlycoShape database counts over 500 unique glycans so far, covering the human glycome and augmented by elements from a wide range of organisms, obtained from 1 ms of cumulative sampling from molecular dynamics simulations. These structures can be linked to proteins with a robust algorithm named Re-Glyco, directly compatible with structural data in open-access repositories, such as the Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) and AlphaFold Protein Structure Database, or own. The quality, performance and broad applicability of GlycoShape is demonstrated by its ability to predict N-glycosylation occupancy, scoring a 93% agreement with experiment, based on screening all proteins in the PDB with a corresponding glycoproteomics profile, for a total of 4,259 N-glycosylation sequons.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.