RING-PyMOL

RING-PyMOL analyzes structural ensembles and molecular dynamics (MD) simulations within PyMOL by constructing and visualizing residue interaction networks. It integrates RING functionalities to map non-covalent interactions and characterize conformational variability in proteins and nucleic acids.

Key Features:

• Residue Interaction Network Mapping: Generates residue interaction networks to identify non-covalent contacts in protein and nucleic acid structures.
• Structural Clustering: Applies clustering methods to group conformational states from structural ensembles and MD trajectories.
• High-Throughput Trajectory Processing: Processes hundreds of structural models and large MD trajectories with optimized performance.
• mmCIF and Typed Interaction Support: Supports mmCIF format and detects typed interactions across proteins and nucleic acids.
• Interactive Analytical Outputs: Produces plots and data files for downstream structural and network analysis.

Scientific Applications:

• Allostery and Conformational Dynamics Analysis: Enables investigation of interaction networks, active site dynamics, and structural heterogeneity in biomolecular systems.

Methodology:

RING-PyMOL parses structural coordinates from ensembles or MD trajectories, computes residue interaction networks based on non-covalent contacts, performs structural clustering to identify recurrent conformations, and visualizes interaction patterns within the PyMOL environment.