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:
ProDy is available under GNU General Public License version 3. 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.