GS-align

GS-align performs glycan structure alignment and computes a size-independent structural similarity score (GS-score) to quantify relationships between glycan structures.

Key Features:

• Iterative maximum clique search: Generates candidate correspondences between two glycan structures using an iterative maximum clique search strategy.
• Fragment superposition: Constructs alignments by superposing glycan fragments to evaluate structural fits.
• GS-score: Determines the optimal alignment using a maximum structural similarity score that is size-independent.
• Exploration of configurations: Evaluates multiple structural configurations to identify the highest-similarity alignment.
• Benchmark validation: Validated on Protein Data Bank (PDB) datasets focusing on N-linked glycans and homologous/non-homologous N-glycoprotein sets.
• Template-based prediction support: Applied to template-based glycan structure prediction workflows.
• Monosaccharide substitution matrices: Applied to generation of monosaccharide substitution matrices from aligned glycan data.

Scientific Applications:

• Glycan structural comparison: Quantifies structural similarity between glycans irrespective of molecular size using the GS-score.
• Template-based glycan structure prediction: Informs prediction of glycan structures by aligning query glycans to template structures.
• Monosaccharide substitution matrix generation: Derives substitution matrices for monosaccharides from aligned glycan datasets.
• N-linked glycan and glycoprotein analysis: Compares and analyzes structural relationships within N-linked glycans and homologous/non-homologous N-glycoprotein sets.

Methodology:

Generate potential alignments via iterative maximum clique search and fragment superposition, select the optimal alignment by maximizing the GS-score, and validate results against PDB N-linked glycans and homologous/non-homologous N-glycoprotein sets.