ProDy - Protein Dynamics & Structural Biology

ProDy is designed to model the collective motions of proteins. It treats proteins as elastic networks, allowing researchers to predict functional movements and structural flexibility from a single PDB file or an ensemble of structures.

When to Use

• Predicting protein flexibility and collective motions (ANM/GNM).
• Performing Principal Component Analysis (PCA) on structural ensembles or MD trajectories.
• Analyzing structural conservation and co-evolution (Evol).
• Comparing multiple protein structures (Ensemble analysis).
• Identifying hinge regions and rigid domains in proteins.
• Docking preparation and binding site analysis (druggability).
• Filtering MD trajectories based on collective modes.

Reference Documentation

Official docs: http://prody.csb.pitt.edu/
Manual: http://prody.csb.pitt.edu/manual/
Search patterns: prody.parsePDB, prody.ANM, prody.GNM, prody.select, prody.Ensemble