ArticleGlycobiology2019
CHARMM-GUI Glycan Modeler for modeling and simulation of carbohydrates and glycoconjugates.
Article in Glycobiology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 208 papers.
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Who cites it
208 citing papers in PubMed.
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- Structure and Dynamics of the HIV-1 Envelope Protein on the Virion Envelope.Journal of the American Chemical Society · 2026Article
- Glycosylation-modulated conformational diversity in neurotrophin receptors.Biophysical journal · 2026Article
- Canonical Antibodies Adopt Distinct Binding Modes to Recognize Viral Glycan Shields.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Resolving Conformational Preferences of Monosaccharides fromJournal of chemical information and modeling · 2026Article
- Localized Rigidification and Allosteric Modulation Mechanisms of SARS-CoV-2 Spike Neutralization by Class 3 and Class 4 Antibodies at Atomic Resolution: An Integrated Computational Study of Binding, Dynamics, and Allostery.bioRxiv : the preprint server for biology · 2026Article
- A Glycan-Aware Diffusion Model for Carbohydrate and Glycoprotein Structure Prediction.bioRxiv : the preprint server for biology · 2026Article
- Article
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- Molecular dynamics simulations of beta-2-glycoprotein 1 (β2GPI) reveal that post-translational modifications facilitate novel structures.Scientific reports · 2026Article
- Structure and Dynamics of the HIV-1 Envelope Protein on the Virion Envelope.bioRxiv : the preprint server for biology · 2026Article
- Mechanisms of Binding and Immune Escape Resistance for Broadly Neutralizing Antibodies Targeting Distinct Conserved SARS-CoV-2 Spike Epitopes: A Hierarchical Approach Integrating Mutational Profiling and Energy Landscape Analysis.International journal of molecular sciences · 2026Article
- Distinct evolutionary patterns of endemic and emerging parvoviruses and the origin of a new pandemic virus.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Atomistic Insights into Conformations and Solvation Dynamics of Amylose, Dextran, and Pullulan Using Three Force Fields.The journal of physical chemistry. B · 2026Article
- Frustration Landscapes of Broadly Neutralizing SARS-CoV-2 Spike Antibodies Targeting Conserved Epitopes Reveal Energetic Logic of Escape-Proof and Escape-Prone Mechanisms.bioRxiv : the preprint server for biology · 2026Article
- The non-scaffold effects of natural polysaccharides in promoting organ regeneration: a review.Journal of biological engineering · 2026Review
- Structural insights into the Thermus thermophilus type IV pilus machinery assembling two distinct pili.Communications biology · 2026Article
- Germline-somatic residue synergy reshapes antibody encounter-state pathways to enhance HIV-1 recognition.bioRxiv : the preprint server for biology · 2026Article
- Exploring the diverse binding ability of SARS-CoV-2 variant RBDs to different antibody classes: a computational study.RSC advances · 2026Article
148 more citing papers are in PubMed but not listed here.
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Authors and funding
10 authors.
Funding
Abstract
Characterizing glycans and glycoconjugates in the context of three-dimensional structures is important in understanding their biological roles and developing efficient therapeutic agents. Computational modeling and molecular simulation have become an essential tool complementary to experimental methods. Here, we present a computational tool, Glycan Modeler for in silico N-/O-glycosylation of the target protein and generation of carbohydrate-only systems. In our previous study, we developed Glycan Reader, a web-based tool for detecting carbohydrate molecules from a PDB structure and generation of simulation system and input files. As integrated into Glycan Reader in CHARMM-GUI, Glycan Modeler (Glycan Reader & Modeler) enables to generate the structures of glycans and glycoconjugates for given glycan sequences and glycosylation sites using PDB glycan template structures from Glycan Fragment Database (http://glycanstructure.org/fragment-db). Our benchmark tests demonstrate the universal applicability of Glycan Reader & Modeler to various glycan sequences and target proteins. We also investigated the structural properties of modeled glycan structures by running 2-μs molecular dynamics simulations of HIV envelope protein. The simulations show that the modeled glycan structures built by Glycan Reader & Modeler have the similar structural features compared to the ones solved by X-ray crystallography. We also describe the representative examples of glycoconjugate modeling with video demos to illustrate the practical applications of Glycan Reader & Modeler. Glycan Reader & Modeler is freely available at http://charmm-gui.org/input/glycan.
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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.