pyFoldX: enabling biomolecular analysis and engineering along structural ensembles

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.

Automated summary

In recent years, there has been an increase in the availability of protein structures, not only for new proteins but also for the same protein crystallized with different molecules or proteins. While protein design software has been successful, it can be sensitive to small conformational differences between structures of the same protein. To address this issue, the authors introduce pyFoldX, a Python library that allows the integrative analysis of structures of the same protein using FoldX. The library offers new functionalities for handling different structures of the same protein, an improved molecular parametrization module, and seamless integration with the Python programming language's data analysis ecosystem.