gRINN

gRINN computes pairwise residue interaction energies from atomistic molecular dynamics (MD) simulation trajectories and constructs protein energy networks to analyze residue-level energetics and network metrics.

Key Features:

• Residue Interaction Energy Analysis: Calculates pairwise residue-residue interaction energies from atomistic MD trajectories.
• Energy Correlation Analysis: Performs energy correlation analysis among residues to identify cooperative energetic relationships.
• Interaction Energy Outputs: Produces interaction energy time-series, distributions, matrices, and correlation networks.
• Protein Energy Network Construction and Analysis: Constructs protein energy networks and computes network metrics including degrees, betweenness centralities, closeness centralities, and shortest path analysis.
• Integration with MD Simulation Packages: Integrates with NAMD and GROMACS and automates extraction of residue-residue interaction energies from user-supplied trajectories.

Scientific Applications:

• Protein dynamics analysis: Identifies critical residue interactions that influence protein stability and function from MD simulations.
• Hypothesis generation and experimental design: Supports generation of hypotheses and design of wet-lab experiments based on residue energetics and network analyses.
• Interpretation of MD simulation data: Automates extraction and analysis of residue interaction energies to facilitate deriving conclusions from MD trajectories.

Methodology:

Calculates pairwise residue interaction energies from atomistic MD trajectories (e.g., NAMD, GROMACS), performs energy correlation analysis, constructs protein energy networks, and computes network metrics including degrees, betweenness and closeness centralities and shortest path analysis.