ArticleStructure (London, England : 1993)2019
Automatically Fixing Errors in Glycoprotein Structures with Rosetta.
Article in Structure (London, England : 1993), 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 88 papers.
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Who cites it
88 citing papers in PubMed.
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- Molecular basis of convergent evolution of ACE2 receptor utilization among HKU5 coronaviruses.Cell · 2025Article
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- Anti-immune complex antibodies are elicited during repeated immunization with HIV Env immunogens.Science immunology · 2025Article
- Glycan masking in immunogen design: computational and experimental methods.Frontiers in immunology · 2025Review
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- Isolation and escape mapping of broadly neutralizing antibodies against emerging delta-coronaviruses.Immunity · 2024Article
- Design of customized coronavirus receptors.Nature · 2024Article
- Computational design of prefusion-stabilized Herpesvirus gB trimers.bioRxiv : the preprint server for biology · 2024Article
- Molecular basis of convergent evolution of ACE2 receptor utilization among HKU5 coronaviruses.bioRxiv : the preprint server for biology · 2024Article
- Article
28 more citing papers are in PubMed but not listed here.
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8 authors.
Funding
Abstract
Recent advances in single-particle cryo-electron microscopy (cryoEM) have resulted in determination of an increasing number of protein structures with resolved glycans. However, existing protocols for the refinement of glycoproteins at low resolution have failed to keep up with these advances. As a result, numerous deposited structures contain glycan stereochemical errors. Here, we describe a Rosetta-based approach for both cryoEM and X-ray crystallography refinement of glycoproteins that is capable of correcting conformational and configurational errors in carbohydrates. Building upon a previous Rosetta framework, we introduced additional features and score terms enabling automatic detection, setup, and refinement of glycan-containing structures. We benchmarked this approach using 12 crystal structures and showed that glycan geometries can be automatically improved while maintaining good fit to the crystallographic data. Finally, we used this method to refine carbohydrates of the human coronavirus NL63 spike glycoprotein and of an HIV envelope glycoprotein, demonstrating its usefulness for cryoEM refinement.
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