ArticlePLoS computational biology2013
Restricted N-glycan conformational space in the PDB and its implication in glycan structure modeling.
Article in PLoS computational biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 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
15 citing papers in PubMed, 34 citations in OpenAlex.
- Glycans in Virus-Host Interactions: A Structural Perspective.Frontiers in molecular biosciences · 2021Review
- Dissecting the conformation of glycans and their interactions with proteins.Journal of biomedical science · 2020Review
- CHARMM-GUI Glycan Modeler for modeling and simulation of carbohydrates and glycoconjugates.Glycobiology · 2019Article
- Conformational Heterogeneity of the HIV Envelope Glycan Shield.Scientific reports · 2017Article
- Identification and Characterization of Complex Glycosylated Peptides Presented by the MHC Class II Processing Pathway in Melanoma.Journal of proteome research · 2017Article
- Delineating the conformational flexibility of trisaccharides from NMR spectroscopy experiments and computer simulations.Physical chemistry chemical physics : PCCP · 2016Article
- Preferred conformations of N-glycan core pentasaccharide in solution and in glycoproteins.Glycobiology · 2016Article
- GS-align for glycan structure alignment and similarity measurement.Bioinformatics (Oxford, England) · 2015Article
- Enhanced conformational sampling using replica exchange with concurrent solute scaling and hamiltonian biasing realized in one dimension.Journal of chemical theory and computation · 2015Article
- Revealing the Mechanisms of Protein Disorder and N-Glycosylation in CD44-Hyaluronan Binding Using Molecular Simulation.Frontiers in immunology · 2015Review
- Article
- Glyco-epitope Diversity: An Evolving Area of Glycomics Research and Biomarker Discovery.Journal of proteomics & bioinformatics · 2014Article
- PTM-SD: a database of structurally resolved and annotated posttranslational modifications in proteins.Database : the journal of biological databases and curation · 2014Article
- Molecular mechanisms of inhibition of influenza by surfactant protein D revealed by large-scale molecular dynamics simulation.Biochemistry · 2013Article
- 'Naked' and hydrated conformers of the conserved core pentasaccharide of N-linked glycoproteins and its building blocks.Journal of the American Chemical Society · 2013Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 2 institutions in 1 country.
Funding
Abstract
Understanding glycan structure and dynamics is central to understanding protein-carbohydrate recognition and its role in protein-protein interactions. Given the difficulties in obtaining the glycan's crystal structure in glycoconjugates due to its flexibility and heterogeneity, computational modeling could play an important role in providing glycosylated protein structure models. To address if glycan structures available in the PDB can be used as templates or fragments for glycan modeling, we present a survey of the N-glycan structures of 35 different sequences in the PDB. Our statistical analysis shows that the N-glycan structures found on homologous glycoproteins are significantly conserved compared to the random background, suggesting that N-glycan chains can be confidently modeled with template glycan structures whose parent glycoproteins share sequence similarity. On the other hand, N-glycan structures found on non-homologous glycoproteins do not show significant global structural similarity. Nonetheless, the internal substructures of these N-glycans, particularly, the substructures that are closer to the protein, show significantly similar structures, suggesting that such substructures can be used as fragments in glycan modeling. Increased interactions with protein might be responsible for the restricted conformational space of N-glycan chains. Our results suggest that structure prediction/modeling of N-glycans of glycoconjugates using structure database could be effective and different modeling approaches would be needed depending on the availability of template 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.