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Related Experiment Video

Updated: Sep 15, 2025

Hierarchical and Programmable One-Pot Oligosaccharide Synthesis

Hierarchical and Programmable One-Pot Oligosaccharide Synthesis

Published on: September 6, 2019

Generating 3D Models of Carbohydrates with GLYCAM-Web.

Oliver C Grant¹, Daniel Wentworth¹, Samuel G Holmes¹

¹Complex Carbohydrate Research Center and Department of Biochemistry and Molecular Biology, University of Georgia, 315 Riverbend Road, Athens, Georgia 30602, United States.

Biorxiv : the Preprint Server for Biology

|July 14, 2025

Summary

This summary is machine-generated.

GLYCAM-Web provides accessible tools for predicting carbohydrate 3D structures, generating accurate models for research and molecular dynamics simulations. These builders ensure rapid and reliable structure generation for complex oligosaccharides.

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Last Updated: Sep 15, 2025

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3D Printing of Biomolecular Models for Research and Pedagogy

3D Printing of Biomolecular Models for Research and Pedagogy

Published on: March 13, 2017

Area of Science:

Carbohydrate Chemistry
Computational Chemistry
Structural Biology

Background:

Carbohydrate 3D structure prediction is crucial for understanding biological roles.
Existing tools may lack experimental consistency or user-friendliness.
GLYCAM-Web offers specialized tools for oligosaccharide structure generation.

Purpose of the Study:

To present the GLYCAM-Web carbohydrate structure-prediction tools (builders).
To highlight their utility in generating experimentally-consistent 3D oligosaccharide structures.
To detail the features enabling data interpretation, hypothesis generation, and molecular dynamics (MD) simulations.

Main Methods:

Utilizes a graphical user interface (GUI) for inputting carbohydrate sequences.
Converts sequences into 3D models in formats like PDB and OFF.
Employs energy minimization using the GLYCAM forcefield and optimized algorithms.
Offers advanced options for rotamer selection and explicit solvation for MD simulations.

Main Results:

Generates experimentally-consistent 3D structures of oligosaccharides.
Provides structures in multiple formats suitable for various downstream applications.
Ensures energy-minimized structures for improved accuracy.
Delivers 3D structures for large oligosaccharides (e.g., 100 residues) in under a minute.

Conclusions:

GLYCAM-Web builders are efficient and scalable tools for oligosaccharide 3D structure prediction.
The tools facilitate diverse research applications, including molecular dynamics simulations.
Integration of conformational preferences and the GLYCAM forcefield ensures reliable structure generation.