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GlyContact analyzes glycan 3D structures at scale.

Luc Thomès1, Roman Joeres2,3,4, Zeynep Akdeniz2,3

  • 1University Lille, CHU Lille, ULR 7364 - RADEME - Maladies RAres du DÉveloppement embryonnaire et du Métabolisme, Lille, France.

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|December 12, 2025
PubMed
Summary

GlyContact is a new Python package for analyzing 3D glycan structures. It helps understand how glycan structure impacts function and improves predictions of lectin-glycan binding.

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Area of Science:

  • Carbohydrate chemistry and structural biology.
  • Computational glycobiology and bioinformatics.

Background:

  • Glycans are complex biomolecules with challenging structural characterization, hindering the understanding of their structure-function relationships.
  • Existing databases like GlycoShape offer 3D glycan structures from simulations, but tools for their analysis are needed.

Purpose of the Study:

  • To introduce GlyContact, an open-source Python package for retrieving, processing, and analyzing 3D glycan structures.
  • To demonstrate GlyContact's utility in exploring glycan structural dynamics and their impact on biological interactions.

Main Methods:

  • Development of the GlyContact Python package for glycan structure analysis.
  • Utilizing molecular dynamics (MD) simulations, NMR, and X-ray crystallography data.
  • Application of von Mises graph neural networks for predicting disaccharide torsion angle distributions.

Main Results:

  • GlyContact reveals the influence of sequence context on glycan motif structure.
  • The package provides insights into glycan flexibility and surface accessibility, improving lectin-binding prediction by approximately 7%.
  • Accurate prediction of torsion angle distributions between disaccharides was achieved.

Conclusions:

  • GlyContact facilitates the exploration of 3D glycan structures, offering valuable insights into their biological functions.
  • The tool enhances the understanding of glycan-lectin interactions and structural dynamics.
  • GlyContact is an open-access resource empowering researchers in glycobiology.