ProDy: Protein Dynamics Analysis

2.6.1 verified Mon Apr 27 auth: no python

ProDy is an open-source Python package for protein dynamics analysis, including structure analysis, normal mode analysis (ANM, GNM, PCA), sequence analysis, trajectory parsing, and protein-ligand interactions. Current version 2.6.1 supports Python >=3.10, NumPy 2, and Python 3.12. Releases occur roughly every few months with bug fixes and new features.

pip install prody

Common errors

error ModuleNotFoundError: No module named 'prody' ↓

cause ProDy not installed or installed in wrong environment.

fix

Run pip install prody in the correct Python environment.

error ImportError: numpy.core.multiarray failed to import ↓

cause NumPy version incompatible with ProDy (e.g., NumPy 2 with ProDy <2.6.0).

fix

Upgrade ProDy: pip install --upgrade prody or downgrade NumPy: pip install 'numpy<2'

error AttributeError: module 'prody' has no attribute 'parsePDB' ↓

cause ProDy not imported correctly (e.g., `import prody` instead of `from prody import parsePDB`).

fix

Use from prody import parsePDB or import prody; pdb = prody.parsePDB(...)

error ValueError: 4-letter PDB ID is not supported ↓

cause ProDy <2.6.0 does not support extended PDB IDs (4-letter codes).

fix

Upgrade to ProDy >=2.6.0: pip install --upgrade prody

Warnings

breaking Python 3.11 or earlier and Python 3.13+ are not supported; requires Python >=3.10 and <3.13. ↓

fix Use Python 3.10-3.12. Check with `python --version`.

breaking NumPy 2 support introduced in v2.6.0; earlier versions may fail with NumPy 2. ↓

fix Upgrade ProDy to v2.6.0+ or pin NumPy <2.

deprecated The `imp.find_module` workaround in apps is removed; use `importlib`. ↓

fix If using custom scripts that relied on `prody.apps`, update to avoid deprecated module loading.

gotcha ProDy uses a global logger that may override your logging level. Call `prody.LOGGER.setLevel(logging.WARNING)` to suppress verbose output. ↓

fix Add `import logging; prody.LOGGER.setLevel(logging.WARNING)` at the start of your script.

gotcha Wildcard import `from prody import *` pollutes namespace with many internal symbols; prefer explicit imports. ↓

fix Use explicit imports: `from prody import parsePDB, ANM, ...`

Install

conda install -c conda-forge prody

Imports

parsePDB
wrong
```
import prody; prody.parsePDB()
```
correct
```
from prody import parsePDB
```
Function is in top-level prody namespace after import

ANM

wrong

from prody.proteins import ANM

correct

from prody import ANM

ANM is in top-level namespace

calcRMSD

wrong

from prody.measure import calcRMSD

correct

from prody import calcRMSD

Direct import from prody is preferred

Quickstart

Parse a PDB, build ANM Hessian, and compute normal modes.

from prody import *
from prody import parsePDB, ANM, calcModes
pdb = parsePDB('1ake')
anm = ANM('example')
anm.buildHessian(pdb)
modes = calcModes(anm)
print(modes[:3])