ensemblify

Author(s):

Nuno P. Fernandes

Year:

2026

Copyright:

GNU Public License v3

A Python library for generating and analyzing ensembles of protein structures.

Main Features

  • Create full-length protein structures by fusing PDB structures of folded protein domains with disordered regions.

  • Generate protein conformational ensembles by changing flexible regions.

  • Convert generated ensembles to trajectory file format.

  • Calculate theoretical SAXS curves from generated ensembles.

  • Analyze generated ensemble’s structural properties through interactive plots.

  • Reweight generated ensembles using experimental data.

  • Re-analyze structural properties of generated ensembles using weights calculated from experimental data, compare to non-reweighted structural properties.

How to access documentation

Documentation is available in two forms:

Use the built-in help function to view a function or module’s docstring:

>>> import ensemblify as ey
>>> help(ey)
>>> help(ey.generation)
>>> help(ey.generation.generate_ensemble)

Available subpackages

modelling

Create full-length protein structures by fusing PDB structures with disordered regions.

generation

Generate an ensemble of structures.

conversion

Convert ensembles to trajectory files and from these calculate SAXS curves.

analysis

Calculate and plot data describing your ensemble.

reweighting

Reweight a generated ensemble using experimental data.

utils

Auxilliary functions used by other modules.

Utilities

show_config()

View Ensemblify’s current general configuration.

update_config()

Update Ensemblify’s current general configuration.

Citation

When using Ensemblify in published work, please cite

PUB

Submodules