TUTORIAL, EXAMPLES, and DOCUMENTATION
-------------------------------------

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

SYNOPSIS
--------

ProDy is a free and open-source Python package for analyzing protein structural 
dynamics. It allows for quantitative analysis of heterogeneous experimental 
structural datasets and comparison with theoretically predicted conformational 
dynamics. It is designed and developed by Ahmet Bakan in Bahar lab at the 
University of Pittsburgh.

The following are some of the main features:

**Examination and analysis of structural variability observed in experiments:**

  * Fast and flexible parsing of PDB and DCD files
  * Powerful atom selections and contact identification
  * Matching, superposing, and comparing multiple structures/chains
  * PCA of X-ray structures, NMR models and mixed structural datasets 
    from Blast search

**Prediction and analysis of protein dynamics using theory and simulation:**

  * Normal Mode Analysis using the Anisotropic network model (ANM)
  * Gaussian network model (GNM) analysis
  * Distance and property dependent force constant functions
  * Essential dynamics analysis (EDA) of MD snapshots
  * Comparative analysis and visualization of dynamics

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 Python Software Foundation License.  

DOWNLOADS & INSTALLATION
------------------------
  
* http://www.csb.pitt.edu/ProDy/getprody.html
* INSTALL.txt

CHANGES
-------

* http://www.csb.pitt.edu/ProDy/changes.html
* CHANGES.txt

SOURCE
------

* http://github.com/abakan/ProDy

EMAILING LIST
-------------

* http://groups.google.com/group/prody-dev

REPORT ISSUES
-------------

* https://github.com/abakan/ProDy/issues
  
