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A Python Package for Protein Dynamics Analysis
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README.rst

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 the Python Software Foundation License.

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