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:
- 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 TreeConstruction 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 (https://github.com/pyparsing/pyparsing) 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).
CEalign module (https://pymolwiki.org/index.php/Cealign_plugin) is distributed with ProDy. The original CE method was developed by Ilya Shindyalov and Philip Bourne. The Python version which is used by ProDy is developed by Jason Vertrees and available under the New BSD license.
Hbp module: The calculation of hydrophobic interactions, solvent accessible surface area (SASA) and volume for each residue is using geometric methods based on the information of the atoms in the molecule. The methods have been programmed in C++ and can be compiled as a python module “hpb.so” which is then used by ProDy. Files for compilation are stored at prody/proteins/hpbmodule folder and required C++ and Fortran compiler. After compilation hpb.so file can be stored in prody/proteins folder in ProDy or in the local directory which is used to perform calulations. The precompiled versions for Python 2.7, 3.8, 3.9, and 3.10 are availabe in prody/proteins/hpbmodule. The user can choose the correct version of hpb.so and copy to the prody/proteins or local directory. C++ code of hpb.so was developed by Xin Cao and Fortran code by Xin Cao, Michelle H. Hummel, Bihua Yu, and Evangelos A. Coutsias (License in prody/proteins/hpbmodule folder). Details of the method can be found in the Supplementary Material of InSty manuscript (soon will be submitted for publication).