LigAlign

LigAlign performs flexible ligand alignment and automated fragmentation to identify conserved structural motifs in protein–ligand complexes.

Key Features:

• Flexible Alignment Capability: Performs alignments treating ligands as flexible entities to account for ligand conformational variability in protein–ligand complexes.
• Automated Fragmentation Process: Generates biochemically reasonable ligand fragmentations automatically to enable flexible alignment and motif detection.
• Consistency with Manual Annotations: Produces rigid-alignment results that are consistent with manually annotated structural motifs.

Scientific Applications:

• Drug Discovery: Identifies conserved ligand structural motifs across complexes to inform ligand design and optimization.
• Molecular Biology and Structural Analysis: Elucidates ligand binding mechanisms and conserved interaction motifs in protein–ligand complexes.

Methodology:

Performs an initial alignment treating ligands as flexible entities, achieves flexibility via automated ligand fragmentation, and can perform rigid alignments that are comparable to manual annotations.