ProDy 1.4

A Python Package for Protein Dynamics Analysis

SYNOPSIS

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.

GETTING PRODY

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

• http://www.csb.pitt.edu/ProDy/getprody.html

DOCUMENTATION

• Homepage: http://www.csb.pitt.edu/ProDy

• Examples: http://www.csb.pitt.edu/ProDy/examples

• Tutorial: http://www.csb.pitt.edu/ProDy/tutorial

• Reference: http://www.csb.pitt.edu/ProDy/reference

• Applications: http://www.csb.pitt.edu/ProDy/apps

• NMWiz GUI: http://www.csb.pitt.edu/NMWiz

• Changes: http://www.csb.pitt.edu/ProDy/changes.html

SOURCE CODE

• Source code: https://bitbucket.org/abakan/prody

• Issue tracker: https://bitbucket.org/abakan/prody/issues

LICENSE

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 the ProDy package. Biopython is developed by The Biopython Consortium and is available under the Biopython license (http://www.biopython.org/DIST/LICENSE).

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

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