Installation

Release Notes

v2.4.1 series come with new and improved sequence, structure, and dynamics analysis features. See release notes for details.

How to Cite

Bakan A, Meireles LM, Bahar I ProDy: Protein Dynamics Inferred from Theory and Experiments
Bioinformatics 2011 27(11):1575-1577.

Bakan A, Dutta A, Mao W, Liu Y, Chennubhotla C, Lezon TR, Bahar I Evol and ProDy for Bridging Protein Sequence Evolution and Structural Dynamics
Bioinformatics 2014 30(18):2681-2683.

Zhang S, Krieger JM, Zhang Y, Kaya C, Kaynak B, Mikulska-Ruminska K, Doruker P, Li H, Bahar I ProDy 2.0: Increased scale and scope after 10 years of protein dynamics modelling with Python
Bioinformatics 2021 37(20):3657-3659.

Installation¶

Required Software¶

Python 2.7, 3.6 or later. We recommend using Anaconda, which provides the conda package and environment manager as well as many useful packages.

NumPy 1.10 or later
SciPy - we recommend that you use the latest version, but all versions should be supported.

Biopython - we recommend that you use the latest version, but all versions should be supported.

When compiling from source, on Linux for example, you will need a C compiler (e.g. gcc) and Python developer libraries (i.e. python.h). If you don’t have Python developer libraries installed on your machine, use your package manager to install python-dev package.

In addition, matplotlib is required for using plotting functions. ProDy, ProDy Applications, and Evol Applications can be operated without this package.

Quick Install¶

If you have pip installed, type the following:

pip install -U ProDy

If you don’t have pip, please download an installation file and follow the instructions.

If you have conda installed, you can also type the following instead:

conda install ProDy

Download & Install¶

After installing the required packages, you will need to download a suitable ProDy source or installation file from http://python.org/pypi/ProDy. For changes and list of new features see Release Notes.

Linux

Download ProDy-x.y.z.tar.gz. Extract tarball contents and run setup.py as follows:

$ tar -xzf ProDy-x.y.z.tar.gz
$ cd ProDy-x.y.z
$ python setup.py build
$ python setup.py install

If you need root access for installation, try sudo python setup.py install. If you don’t have root access, please consult alternate and custom installation schemes in Installing Python Modules.

Mac OS

For installing ProDy, please follow the Linux installation instructions.

Windows

Remove previously installed ProDy release from Uninstall a program in Control Panel.

Download ProDy-1.x.y.win32-py2.z.exe and run to install ProDy.

To be able use ProDy Applications and Evol Applications in command prompt (cmd.exe), append Python and scripts folders (e.g. C:\Python27 and C:\Python27\Scripts) to PATH environment variable.

Recommended Software¶

`Scipy`_, when installed, replaces linear algebra module of Numpy. Scipy linear algebra module is more flexible and can be faster.
IPython is a must have for interactive ProDy sessions.
PyReadline for colorful IPython sessions on Windows.
MDAnalysis or MDTraj for reading molecular dynamics trajectories.

Included in ProDy¶

Following software is included in the ProDy installation packages:

pyparsing is used to define the atom selection grammar.
`Biopython`_ KDTree package and pairwise2 module are used for distance based atom selections and pairwise sequence alignment, respectively.
argparse is used to implement applications and provided for compatibility with Python 2.6.

Source Code¶

Source code is available at https://github.com/prody/ProDy.