ArticleGlycobiology2021
Modernized uniform representation of carbohydrate molecules in the Protein Data Bank.
Article in Glycobiology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
21 citing papers in PubMed.
- Physical Implausibility of Carbohydrate Ligands in Results of Deep Learning-Based Cofolding Methods.Journal of chemical information and modeling · 2026Article
- Generating 3D models of complex carbohydrates with GLYCAM-Web.Nature methods · 2026Article
- GlyContact analyzes glycan 3D structures at scale.Nature communications · 2025Article
- Modeling glycans with AlphaFold 3: capabilities, caveats, and limitations.Glycobiology · 2025Article
- Surface Plasmon Resonance for the Interaction of Capsular Polysaccharide (CPS) With KpACE.Bio-protocol · 2025Article
- Visualizing and analyzing 3D biomolecular structures using Mol* at RCSB.org: Influenza A H5N1 virus proteome case study.Protein science : a publication of the Protein Society · 2025Article
- PDBe tools for an in-depth analysis of small molecules in the Protein Data Bank.Protein science : a publication of the Protein Society · 2025Article
- Functional implications of glycans and their curation: insights from the workshop held at the 16th Annual International Biocuration Conference in Padua, Italy.Database : the journal of biological databases and curation · 2024Article
- Announcing the launch of Protein Data Bank China as an Associate Member of the Worldwide Protein Data Bank Partnership.Acta crystallographica. Section D, Structural biology · 2023Article
- The catalytic domains of Streptococcus mutans glucosyltransferases: a structural analysis.Acta crystallographica. Section F, Structural biology communications · 2023Article
- Electron microscopy holdings of the Protein Data Bank: the impact of the resolution revolution, new validation tools, and implications for the future.Biophysical reviews · 2022Review
- RCSB Protein Data bank: Tools for visualizing and understanding biological macromolecules in 3D.Protein science : a publication of the Protein Society · 2022Article
- Protein Data Bank: A Comprehensive Review of 3D Structure Holdings and Worldwide Utilization by Researchers, Educators, and Students.Biomolecules · 2022Review
- Exploring protein symmetry at the RCSB Protein Data Bank.Emerging topics in life sciences · 2022Article
- PDBx/mmCIF Ecosystem: Foundational Semantic Tools for Structural Biology.Journal of molecular biology · 2022Review
- Simplified quality assessment for small-molecule ligands in the Protein Data Bank.Structure (London, England : 1993) · 2022Article
- RCSB Protein Data Bank resources for structure-facilitated design of mRNA vaccines for existing and emerging viral pathogens.Structure (London, England : 1993) · 2022Article
- PDB-101: Educational resources supporting molecular explorations through biology and medicine.Protein science : a publication of the Protein Society · 2022Article
- RCSB Protein Data Bank: Celebrating 50 years of the PDB with new tools for understanding and visualizing biological macromolecules in 3D.Protein science : a publication of the Protein Society · 2022Article
- SugarDrawer: A Web-Based Database Search Tool with Editing Glycan Structures.Molecules (Basel, Switzerland) · 2021Article
Corrections and comments
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Authors and funding
10 authors.
Funding
Abstract
Since 1971, the Protein Data Bank (PDB) has served as the single global archive for experimentally determined 3D structures of biological macromolecules made freely available to the global community according to the FAIR principles of Findability-Accessibility-Interoperability-Reusability. During the first 50 years of continuous PDB operations, standards for data representation have evolved to better represent rich and complex biological phenomena. Carbohydrate molecules present in more than 14,000 PDB structures have recently been reviewed and remediated to conform to a new standardized format. This machine-readable data representation for carbohydrates occurring in the PDB structures and the corresponding reference data improves the findability, accessibility, interoperability and reusability of structural information pertaining to these molecules. The PDB Exchange MacroMolecular Crystallographic Information File data dictionary now supports (i) standardized atom nomenclature that conforms to International Union of Pure and Applied Chemistry-International Union of Biochemistry and Molecular Biology (IUPAC-IUBMB) recommendations for carbohydrates, (ii) uniform representation of branched entities for oligosaccharides, (iii) commonly used linear descriptors of carbohydrates developed by the glycoscience community and (iv) annotation of glycosylation sites in proteins. For the first time, carbohydrates in PDB structures are consistently represented as collections of standardized monosaccharides, which precisely describe oligosaccharide structures and enable improved carbohydrate visualization, structure validation, robust quantitative and qualitative analyses, search for dendritic structures and classification. The uniform representation of carbohydrate molecules in the PDB described herein will facilitate broader usage of the resource by the glycoscience community and researchers studying glycoproteins.
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Registered trials
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