ArticleCanadian journal of chemistry2016
Extension and validation of the GLYCAM force field parameters for modeling glycosaminoglycans.
Article in Canadian journal of chemistry, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 49 papers.
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Who cites it
49 citing papers in PubMed, 86 citations in OpenAlex.
- Glycosaminoglycans in tissue regeneration: Insights into glycobiology and their biomedical application.Bioactive materials · 2026Review
- Comparison of Protein-Glycosaminoglycan Interactions in ff14sb/GLYCAM06j-1 and CHARMM36m Force Fields.Journal of chemical information and modeling · 2026Article
- CCHFV GP38 and GP85 interact with cell-surface glycosaminoglycans.Npj viruses · 2026Article
- Efficient Small-Molecule Reversal Agents for Anticoagulant Fondaparinux.ACS pharmacology & translational science · 2025Article
- Sticky organisms create underwater biological adhesives driven by interactions between EGF- and GlcNAc- containing polysaccharides.Nature communications · 2025Article
- Refinement of the Drude Polarizable Force Field for Hexose Monosaccharides: Capturing Ring Conformational Dynamics with Enhanced Accuracy.Journal of chemical theory and computation · 2024Article
- Developing and Benchmarking Sulfate and Sulfamate Force Field Parameters via Ab Initio Molecular Dynamics Simulations To Accurately Model Glycosaminoglycan Electrostatic Interactions.Journal of chemical information and modeling · 2024Article
- Differential Solvent DEEP-STD NMR and MD Simulations Enable the Determinants of the Molecular Recognition of Heparin Oligosaccharides by Antithrombin to Be Disentangled.International journal of molecular sciences · 2024Article
- Docking and Molecular Dynamics Simulations Clarify Binding Sites for Interactions of Novel Marine Sulfated Glycans with SARS-CoV-2 Spike Glycoprotein.Molecules (Basel, Switzerland) · 2023Article
- Heparan sulfate glycomimeticsChemical science · 2023Article
- Glycosaminoglycans: What Remains To Be Deciphered?JACS Au · 2023Review
- An optimized thermodynamics integration protocol for identifying beneficial mutations in antibody design.Frontiers in immunology · 2023Article
- Chemoenzymatic synthesis of sulfur-linked sugar polymers as heparanase inhibitors.Nature communications · 2022Article
- Atomic-Resolution Experimental Structural Biology and Molecular Dynamics Simulations of Hyaluronan and Its Complexes.Molecules (Basel, Switzerland) · 2022Review
- Molecular dynamics simulations to understand glycosaminoglycan interactions in the free- and protein-bound states.Current opinion in structural biology · 2022Review
- Dynamic Combinatorial Optimization ofJournal of medicinal chemistry · 2022Article
- Characterization of Heparin's Conformational Ensemble by Molecular Dynamics Simulations and Nuclear Magnetic Resonance Spectroscopy.Journal of chemical theory and computation · 2022Article
- Development of a Real-Time Pectic Oligosaccharide-Detecting Biosensor Using the Rapid and Flexible Computational Identification of Non-Disruptive Conjugation Sites (CINC) Biosensor Design Platform.Sensors (Basel, Switzerland) · 2022Article
- In-Depth Molecular Dynamics Study of All Possible Chondroitin Sulfate Disaccharides Reveals Key Insight into Structural Heterogeneity and Dynamism.Biomolecules · 2022Article
- Aqueous Molecular Dynamics for Understanding Glycosaminoglycan Recognition by Proteins.Methods in molecular biology (Clifton, N.J.) · 2022Article
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Authors and funding
8 authors at 1 institution in 1 country.
Funding
Abstract
Glycosaminoglycans (GAGs) are an important class of carbohydrates that serve critical roles in blood clotting, tissue repair, cell migration and adhesion, and lubrication. The variable sulfation pattern and iduronate ring conformations in GAGs influence their polymeric structure and nature of interaction. This study characterizes several heparin-like GAG disaccharides and tetrasaccharides using NMR and molecular dynamics simulations to assist in the development of parameters for GAGs within the GLYCAM06 force field. The force field additions include parameters and charges for a transferable sulfate group for O- and N-sulfation, neutral (COOH) forms of iduronic and glucuronic acid, and Δ4,5-unsaturated uronate (ΔUA) residues. ΔUA residues frequently arise from the enzymatic digestion of heparin and heparin sulfate. Simulations of disaccharides containing ΔUA reveal that the presence of sulfation on this residue alters the relative populations of
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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.