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Provide an integrated environment for structure-based analysis of protein dynamics, comparison, plotting, visualization of experimental and computational data.


ProDy is a free and open-source Python package for analyzing protein structural dynamics. It is designed and developed by Ahmet Bakan in Bahar lab at the University of Pittsburgh. New functional features are continually being added to ProDy. The following are the main features that have been successfully implemented to date:











The following are the main features that have been successfully implemented to date:

* Examination and analysis of structural variability observed in experiments:
- Efficient parsing of PDB files
- Powerful atoms selections and contact identification
- Matching, superposing, and comparing multiple structures/chains
- Principal component analysis (PCA) of X-ray structures
- PCA of NMR models
- PCA of mixed structural datasets from Blast search
* Prediction and analysis of protein dynamics using theory and simulation:
- Normal Mode Analysis using the Anisotropic network models (ANM)
- Gaussian network models (GNM) analysis
- Essential dynamics analysis (EDA) of MD snapshots
- Comparative analysis and visualization of dynamics

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