ArticleNucleic acids research2013
Glycan fragment database: a database of PDB-based glycan 3D structures.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
30 citing papers in PubMed, 51 citations in OpenAlex.
- Cryo-EM structures of Candida albicans chitin synthase Chs1 reveal a druggable translocation channel.Nature microbiology · 2026Article
- Glycoproteomic landscape and structural dynamics of TIM family immune checkpoints enabled by mucinase SmE.Nature communications · 2023Article
- Article
- Conserved topology of virus glycoepitopes presents novel targets for repurposing HIV antibody 2G12.Scientific reports · 2022Article
- CHARMM-GUI Drude prepper for molecular dynamics simulation using the classical Drude polarizable force field.Journal of computational chemistry · 2022Article
- Dual nature of human ACE2 glycosylation in binding to SARS-CoV-2 spike.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Biomechanical characterization of SARS-CoV-2 spike RBD and human ACE2 protein-protein interaction.Biophysical journal · 2021Article
- Three-Dimensional Structures of Carbohydrates and Where to Find Them.International journal of molecular sciences · 2020Review
- The Glycoprotease CpaA Secreted by Medically Relevant Acinetobacter Species Targets MultiplemBio · 2020Article
- GlyMDB: Glycan Microarray Database and analysis toolset.Bioinformatics (Oxford, England) · 2020Article
- Article
- Computational tools for drawing, building and displaying carbohydrates: a visual guide.Beilstein journal of organic chemistry · 2020Review
- CHARMM-GUI Glycan Modeler for modeling and simulation of carbohydrates and glycoconjugates.Glycobiology · 2019Article
- Long-ranged Protein-glycan Interactions Stabilize von Willebrand Factor A2 Domain from Mechanical Unfolding.Scientific reports · 2018Article
- Glycan Reader is improved to recognize most sugar types and chemical modifications in the Protein Data Bank.Bioinformatics (Oxford, England) · 2017Article
- Modeling of Oligosaccharides within Glycoproteins from Free-Energy Landscapes.Journal of chemical information and modeling · 2017Article
- Influence of Ganglioside GM1 Concentration on Lipid Clustering and Membrane Properties and Curvature.Biophysical journal · 2016Article
- Delineating the conformational flexibility of trisaccharides from NMR spectroscopy experiments and computer simulations.Physical chemistry chemical physics : PCCP · 2016Article
- Glycosylation is crucial for a proper catalytic site organization in human glucocerebrosidase.Glycoconjugate journal · 2016Article
- Atomic visualization of a flipped-back conformation of bisected glycans bound to specific lectins.Scientific reports · 2016Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
The glycan fragment database (GFDB), freely available at http://www.glycanstructure.org, is a database of the glycosidic torsion angles derived from the glycan structures in the Protein Data Bank (PDB). Analogous to protein structure, the structure of an oligosaccharide chain in a glycoprotein, referred to as a glycan, can be characterized by the torsion angles of glycosidic linkages between relatively rigid carbohydrate monomeric units. Knowledge of accessible conformations of biologically relevant glycans is essential in understanding their biological roles. The GFDB provides an intuitive glycan sequence search tool that allows the user to search complex glycan structures. After a glycan search is complete, each glycosidic torsion angle distribution is displayed in terms of the exact match and the fragment match. The exact match results are from the PDB entries that contain the glycan sequence identical to the query sequence. The fragment match results are from the entries with the glycan sequence whose substructure (fragment) or entire sequence is matched to the query sequence, such that the fragment results implicitly include the influences from the nearby carbohydrate residues. In addition, clustering analysis based on the torsion angle distribution can be performed to obtain the representative structures among the searched glycan structures.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.