CONAN

CONAN analyzes inter-residue contacts from molecular dynamics (MD) trajectories to characterize biomolecular dynamics and associate contact patterns with functionally relevant states.

Key Features:

• Inter-Residue Contact Analysis: Analyzes inter-residue contacts derived from molecular dynamics (MD) simulations to quantify interaction patterns.
• Time-Resolved Contact Maps: Generates videos of time-resolved contact maps to visualize temporal changes in molecular interactions.
• Correlation and Principal Component Analysis (PCA): Computes correlation matrices and performs PCA to identify correlated contacts and principal modes of contact variation.
• Cluster Analysis: Performs cluster analysis to identify distinct conformational states sampled during dynamics.

Scientific Applications:

• Equilibrium Dynamics Investigation: Analyzes how specific inter-residue contacts contribute to equilibrium behavior of biomolecules.
• Nonequilibrium Dynamics Study: Examines contact changes during nonequilibrium processes and transitions between states.
• Mechanical Unfolding Analysis: Describes dynamics of ubiquitin during mechanical unfolding by monitoring contact rearrangements.
• Conformational Transition Monitoring: Monitors conformational transitions such as α-β transitions in α-synuclein mutant peptides via contact dynamics.

Methodology:

Processes molecular dynamics trajectories to compute inter-residue contacts, generate time-resolved contact map visualizations, and apply correlation analysis, PCA, and cluster analysis.