WONKA

WONKA performs systematic analysis of ensembles of protein-ligand structures to identify conserved and unusual features in protein-ligand interactions.

Key Features:

• Structural coordinate processing: Processes structural coordinates from protein-ligand complexes to enable ensemble-level analysis.
• Summarization of ligand and protein features: Extracts and summarizes key features of ligands and protein binding sites across structural datasets.
• Dataset consolidation: Consolidates large structural datasets, demonstrated on three bromodomain datasets, for comparative analysis.
• Ligand-specific analysis: Relates analyses to individual ligands to identify unusual or erroneous binding modes.

Scientific Applications:

• Structural biology: Comparative analysis of protein-ligand ensembles to characterize conserved binding site features.
• Binding-mode validation: Identification and validation of atypical or erroneous ligand binding modes in structural datasets.
• Ensemble-level anomaly detection: Detection of unusual structural features across multiple complexes within datasets such as bromodomain collections.

Methodology:

WONKA processes structural coordinates and summarizes ligand and protein features, relating analyses to individual ligands to detect conserved and unusual binding patterns.