RING

RING (Residue Interaction Network Generator) constructs and analyzes residue interaction networks (RINs) from three-dimensional biomolecular structures. It converts Protein Data Bank (PDB) and mmCIF files into graphs where nodes represent amino acid residues and edges represent physico-chemical interactions, including hydrogen bonds and van der Waals contacts.

Key Features:

• PDB and mmCIF-Based RIN Construction: Generates physico-chemically validated residue interaction networks from PDB and mmCIF structures, including nucleic acids defined in the PDB chemical component dictionary.
• Structural Parameter Integration: Incorporates secondary structure, solvent accessibility, experimental uncertainty, residue conservation, mutual information, and energy scoring functions into network annotation.
• Probabilistic Graph Modeling: Represents conformational ensembles from NMR or molecular dynamics simulations as weighted edges to analyze structural variability.
• Cytoscape Compatibility: Supports export to Cytoscape for computation of topological network parameters and advanced graph analysis.
• Contact Evolution Analysis: Visualizes interaction changes across models or time using heatmaps.

Scientific Applications:

• Protein Structure and Interaction Analysis: Enables investigation of residue interaction patterns, structural stability, functional sites, and therapeutic target identification.

Methodology:

RING parses atomic coordinates from PDB or mmCIF files, detects physico-chemical contacts between residues, constructs graph representations of residue interaction networks, annotates nodes and edges with structural and evolutionary features, and supports topological and conformational variability analyses.