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 regi…