Arpeggio

Arpeggio calculates and classifies interatomic interactions in protein structures and protein–ligand complexes to characterize molecular recognition and support analysis of mutation effects and structure-based drug design.

Key Features:

• Interaction calculation: Computes a wide array of interatomic interactions within and between macromolecules, including Van der Waals forces, ionic bonds, carbonyl contacts, metal coordination, hydrophobic interactions, halogen bonds, and hydrogen bonds.
• Specific interactions: Identifies atom–aromatic ring and aromatic ring–aromatic ring interactions, including cation-π, donor-π, halogen-π, carbon-π, and π-π stacking.
• Implementation: Implemented in Python.
• Export: Produces PyMOL session files containing annotated interactions for external visualization.

Scientific Applications:

• Drug Design: Enumerates and visualizes interatomic contacts between small molecules and proteins to inform structure-based design and optimization of therapeutics.
• Structural Biology: Elucidates the structural basis of protein–ligand and protein–protein interactions to analyze molecular recognition mechanisms.
• Mutational Analysis: Assesses how mutations alter interatomic contacts within proteins to infer effects on protein function and stability relevant to genetic disease studies.

Methodology:

Arpeggio analyzes macromolecule structures to identify and classify interatomic interactions based on atom type, distance, and angle constraints.