pyFoldX: enabling biomolecular analysis and engineering along structural ensembles

Bioinformatics. 2022 Apr 12;38(8):2353-2355. doi: 10.1093/bioinformatics/btac072.


Summary: Recent years have seen an increase in the number of structures available, not only for new proteins but also for the same protein crystallized with different molecules and proteins. While protein design software has proven to be successful in designing and modifying proteins, they can also be overly sensitive to small conformational differences between structures of the same protein. To cope with this, we introduce here pyFoldX, a python library that allows the integrative analysis of structures of the same protein using FoldX, an established forcefield and modelling software. The library offers new functionalities for handling different structures of the same protein, an improved molecular parametrization module and an easy integration with the data analysis ecosystem of the python programming language.

Availability and implementation: pyFoldX rely on the FoldX software for energy calculations and modelling, which can be downloaded upon registration in and its licence is free of charge for academics. The pyFoldX library is open-source. Full details on installation, tutorials covering the library functionality and the scripts used to generate the data and figures presented in this paper are available at

Supplementary information: Supplementary data are available at Bioinformatics online.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Ecosystem*
  • Gene Library
  • Programming Languages
  • Proteins
  • Software*


  • Proteins