GlyLES

GlyLES converts glycans from IUPAC-condensed notation into SMILES strings to represent atomic-level glycan structures for computational analysis.

Key Features:

• Grammar-based parsing: Employs a grammar-based approach to interpret IUPAC-condensed notation and extract glycan structure information.
• Monomer tree construction: Constructs a monomer tree representation of the glycan topology from the parsed IUPAC-condensed input.
• Atomic structure computation: Computes atomic structures for each monomer based on their IUPAC-condensed descriptions.
• SMILES generation: Merges computed monomer structures into a complete glycan representation exported as a SMILES string.

Scientific Applications:

• Visualization and analysis: Provides SMILES representations that enable use of molecular visualization and analysis tools for glycans.
• Substructure search and molecular modeling: Enables substructure searches and integration with molecular modeling workflows using atomic-level representations.
• Docking studies: Supplies SMILES-formatted glycans for docking and interaction studies with other biomolecules.
• Machine learning featurization: Produces SMILES that can be used as features in machine learning models for glycomics analyses.

Methodology:

Parses IUPAC-condensed notation using a grammar-based system to construct a monomer tree, computes atomic structures for each monomer from the IUPAC-condensed descriptions, and merges the monomers into a complete glycan SMILES string.