RINmaker

RINmaker constructs residue interaction networks (RINs) from crystallographic descriptions of proteins to enable graph-based analysis of amino acid contacts and protein topology.

Key Features:

• Graph-based RIN construction: Transforms crystallographic descriptions of proteins into graphs with amino acids as nodes and non-covalent interactions as edges.
• Interaction support: Detects and encodes all standard non-covalent interactions between residues.
• Topological analysis: Computes topological properties of residue interaction networks to characterize protein structure and contacts.
• Customizability and pipeline integration: Provides options for customization and integration into computational analysis pipelines.
• Benchmarking and performance: Has been rigorously benchmarked against existing alternatives for efficiency, performance, and correctness.

Scientific Applications:

• Protein stability and topology analysis: Use RINs to investigate structural stability and topological organization of proteins.
• Protein interactions and dynamics: Analyze residue-level interaction networks to study intermolecular and intramolecular contacts and their implications for dynamics.
• Large protein structure analysis: Apply graph-based approaches to characterize large proteins where detailed 3D analyses are cumbersome.
• Integration with data-driven and simulation methods: Combine RIN-derived features with machine learning and numerical simulations of physically motivated models.

Methodology:

Transforms crystallographic descriptions into graph-based representations by representing amino acids as nodes and non-covalent bonds as edges, performs graph/topological analyses of the resulting RINs, and has been benchmarked against existing tools for performance and correctness.