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ProDy is a free and open-source Python package for protein structure, dynamics, and sequence analysis. It allows for comparative analysis and modeling of protein structural dynamics and sequence co-evolution. Fast and flexible ProDy API is for interactive usage as well as application development. ProDy also comes with several analysis applications and a graphical user interface for visual analysis.

You can run ProDy on all major platforms. For download and installation instructions see:

• http://prody.csb.pitt.edu/downloads

• Homepage: http://prody.csb.pitt.edu/
• Tutorials: http://prody.csb.pitt.edu/tutorials
• Reference: http://prody.csb.pitt.edu/manual
• Applications: http://prody.csb.pitt.edu/manual/apps
• NMWiz GUI: http://prody.csb.pitt.edu/nmwiz
• Changes: http://prody.csb.pitt.edu/manual/release

• Source code: https://github.com/prody/ProDy
• Issue tracker: https://github.com/prody/ProDy/issues

ProDy is available under MIT License. See LICENSE.txt for more details.

Biopython (http://biopython.org/) KDTree and pairwise2 modules are distributed with ProDy. Biopython is developed by The Biopython Consortium and is available under the Biopython license (http://www.biopython.org/DIST/LICENSE).

Pyparsing (http://pyparsing.wikispaces.com/) module is distributed with ProDy. Pyparsing is developed by Paul T. McGuire and is available under the MIT license (http://www.opensource.org/licenses/mit-license.php).

Argparse module (http://code.google.com/p/argparse/) is distributed with ProDy. Argparse is developed by Steven J. Bethard and is available under the Python Software Foundation License.