ProDy: Python Package for Protein Dynamics Analysis

ProDy is a free, open-source Python package for analysing protein structure, dynamics and sequence. This page is for computational biologists and lab researchers who need to know what ProDy does, which inputs it reads, how to install it and how to cite it. Facts below come from the ProDy homepage, its GitHub README and its PyPI listing, read on 2026-11-07.

What ProDy is

ProDy (Protein Dynamics) is described by its maintainers as a package for protein structural dynamics analysis, with an API designed for interactive use and for building applications. It is released under the MIT License. The current PyPI release is 2.6.1 (19 August 2025) and requires Python 3.10 or later.

This page covers only the Python package developed by the Bahar group.

Who runs it and what it covers

The project is hosted at bahargroup.org/prody with source code at github.com/prody/ProDy. The README groups the code into modules:

• prody.dynamics: normal mode analysis with elastic network models, principal component analysis (PCA), SignDy, ClustENM, perturbation response scanning and hitting-time analysis.
• prody.sequence: sequence alignment and evolutionary analysis for Evol.
• prody.database: interfaces to CATH, DALI, UniProt and Pfam.
• Other modules: proteins (structure parsing and alignment, InSty, WatFinder), ensemble, chromatin (ChromDy), compounds, domain decomposition (Spectrus) and trajectory.

The homepage lists the input types it handles: PDB files, DCD trajectory files and structural ensembles built from heterogeneous X-ray structures, BLAST-derived sets, NMR models or molecular dynamics snapshots. Analyses include PCA, essential dynamics analysis (EDA), and normal mode analysis with the anisotropic (ANM) and Gaussian (GNM) network models.

How to install it

1. Create or activate a Python 3.10+ environment. The README recommends the Anaconda package manager for handling dependencies; see our guide to installing Anaconda Python.
2. Install from PyPI with pip install ProDy (the PyPI page’s command), or from conda-forge with conda install -c conda-forge ProDy (the README’s command).
3. To build from source, clone the Git repository, run python setup.py build_ext --inplace --force, then pip install -Ue .. The optional compiled hpb module needs a C++ and a Fortran compiler.
4. The homepage names NumPy, SciPy, Biopython, Pyparsing and Matplotlib as libraries ProDy makes use of; Biopython’s KDTree and TreeConstruction modules and pyparsing are bundled in the source.

How to learn the core workflows

The homepage links tutorials in the order most users need them:

1. Structure analysis: parsing PDB files, contacts and structure comparison.
2. Trajectory analysis: reading DCD files and running EDA.
3. Ensemble analysis: X-ray, BLAST and NMR ensembles.
4. ENM analysis: ANM, GNM and distance- or property-dependent force constants (gamma).
5. Evol: conservation and coevolution analysis.
6. NMWiz, InSty and WatFinder tutorials, plus workshop materials.

Applications built on ProDy

Application	Purpose (per the ProDy homepage)
Evol	Comparing sequence evolution with structural dynamics
SignDy	Signature dynamics across protein families
membrANM	Anisotropic network model for membrane proteins
PRS	Perturbation response scanning
ClustENMD	Conformer sampling
ESSA	Essential site identification from frequency shifts
CryoDy	Dynamics of cryo-EM density-derived models
DruGUI	Druggability simulations
NMWiz	VMD plugin that displays ANM and GNM normal modes, with arrows for the slowest modes and animation

NMWiz is the usual bridge to visualisation; see our guides to Visual Molecular Dynamics (VMD) and PyMOL for the viewers themselves.

Strengths and limits

• Strength: one scriptable package covers structure parsing, elastic network models, PCA/EDA and evolutionary analysis, so a single Python script can document the whole workflow, which supports computational reproducibility.
• Strength: permissive MIT licence, source on GitHub, and PyPI plus conda-forge distribution.
• Limit: it is a library for Python users, not a point-and-click tool; the only graphical front end named in the README is the NMWiz plugin for VMD.
• Limit: the older Read the Docs mirror is a partial copy of the 1.9.x manual (release 1.9.4, 2018), so use the homepage tutorials for current features.

Alternatives

Different tools cover neighbouring tasks; this table does not compare performance.

Tool	Relationship to ProDy
Biopython	General bioinformatics library; ProDy bundles some Biopython modules
VMD	Molecular visualisation and trajectory viewer; hosts the NMWiz plugin
PyMOL	Molecular graphics for viewing structures
NetworkX	General Python graph analysis, not protein-specific

How to cite ProDy

The ProDy homepage lists three papers, all in Bioinformatics:

• Zhang S, Krieger JM, Zhang Y, et al. ProDy 2.0: Increased scale and scope after 10 years of protein dynamics modelling with Python. 2021;37(20):3657-3659.
• Bakan A, Meireles LM, Bahar I. ProDy: Protein Dynamics Inferred from Theory and Experiments. 2011;27(11):1575-1577.
• Bakan A, Dutta A, Mao W, et al. Evol and ProDy for Bridging Protein Sequence Evolution and Structural Dynamics. 2014;30(18):2681-2683.

The README lists these papers but does not state which one a user must cite; check the project homepage and the journal’s own guidance when preparing a manuscript.

FAQ

What is ProDy used for?

Analysing protein structure, dynamics and sequence evolution in Python, including normal mode analysis, PCA and ensemble analysis.

How do I install ProDy?

Run pip install ProDy (PyPI) or conda install -c conda-forge ProDy (conda-forge) in a Python 3.10+ environment.

Is ProDy free?

Yes. It is open source under the MIT License; bundled third-party components such as Biopython and pyparsing carry their own licences.

Where is the ProDy source code?

At github.com/prody/ProDy.

Sources

• ProDy homepage, bahargroup.org/prody (read 2026-11-07; page last updated 7 February 2025)
• ProDy README, github.com/prody/ProDy (read 2026-11-07)
• ProDy on PyPI, pypi.org/project/ProDy (read 2026-11-07)