ArticleGlycobiology2019
GAG Builder: a web-tool for modeling 3D structures of glycosaminoglycans.
Article in Glycobiology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 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.
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Who cites it
28 citing papers in PubMed.
- Generating 3D models of complex carbohydrates with GLYCAM-Web.Nature methods · 2026Article
- Designing and Evaluation of a Novel IL-1RA Fusion Cytokine to Enhance the Pharmacokinetics and Receptor Affinity for Better Therapeutic Intervention in Inflammatory Disorders.Current computer-aided drug design · 2026Article
- Production and inhibition of human Heparan 6-O-Endosulfatase SULF1.Glycobiology · 2025Article
- Atomistic Polymer Modeling: Recent Advances and Challenges in Building and Parametrization Workflows.Macromolecules · 2025Review
- Article
- Heparan-6-O-endosulfatase 2, a cancer-related proteoglycan enzyme, is effectively inhibited by a specific sea cucumber fucosylated glycosaminoglycan.Glycobiology · 2025Article
- A novel esterase regulates Klebsiella pneumoniae hypermucoviscosity and virulence.PLoS pathogens · 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
- The Legionella collagen-like protein employs a distinct binding mechanism for the recognition of host glycosaminoglycans.Nature communications · 2024Article
- Article
- Computational toolbox for the analysis of protein-glycan interactions.Beilstein journal of organic chemistry · 2024Review
- A quinolin-8-ol sub-millimolar inhibitor of UGGT, the ER glycoprotein folding quality control checkpoint.iScience · 2023Article
- HS, an Ancient Molecular Recognition and Information Storage Glycosaminoglycan, Equips HS-Proteoglycans with Diverse Matrix and Cell-Interactive Properties Operative in Tissue Development and Tissue Function in Health and Disease.International journal of molecular sciences · 2023Review
- The first laminin G-like domain of protein S is essential for binding and activation of Tyro3 receptor and intracellular signalling.Biochemistry and biophysics reports · 2022Article
- Dynamic Combinatorial Optimization ofJournal of medicinal chemistry · 2022Article
- Aqueous Molecular Dynamics for Understanding Glycosaminoglycan Recognition by Proteins.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Pyranose Ring Puckering Thermodynamics for Glycan Monosaccharides Associated with Vertebrate Proteins.International journal of molecular sciences · 2021Article
- Elucidating the Binding Mode between Heparin and Inflammatory Cytokines by Molecular Modeling.ChemistryOpen · 2021Article
- Sulfation and Calcium Favor Compact Conformations of Chondroitin in Aqueous Solutions.ACS omega · 2021Article
- A Bittersweet Computational Journey among Glycosaminoglycans.Biomolecules · 2021Review
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
Here we report the launch of a web-tool (the GLYCAM-Web GAG Builder, www.glycam.org/gag) for the rapid and straightforward prediction of 3D structural models for glycosaminoglycans (GAGs). The tool provides the user with coordinate files (PDB format) for use in visualization, as well as files for performing MD simulation with the AMBER software package. Counter ions and water may also be added as desired. The tool is designed with the non-expert in mind, and as such has implemented typical default values for structural parameters, which the user may change if desired. Multiple GAG types are supported, including Heparin/Heparan Sulfate, Chondroitin Sulfate, Dermatan Sulfate, Keratan Sulfate, and Hyaluronan; however, the user may alter the default sulfation patterns to create novel sequences. The common non-natural unsaturated uronic acid (ΔUA) and its sulfated derivative are also supported.
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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.