poli.core.util.proteins.foldx

FoldX interface for measuring stability and SASA.

This module implements a FoldxInterface for querying foldx’s repairing and simulating models [1]. This implementation is heavily inspired by the way LaMBO uses FoldX [2].

If this module is imported from a script, it will automatically check that the foldx files are in the expected location, and raise an error if they are not.

References

[1] The FoldX web server: an online force field.

Schymkowitz, J., Borg, J., Stricher, F., Nys, R., Rousseau, F., & Serrano, L. (2005). Nucleic acids research, 33(suppl_2), W382-W388.

[2] “Accelerating Bayesian Optimization for Biological Sequence

Design withDenoising Autoencoders.” Stanton, Samuel, Wesley Maddox, Nate Gruver, Phillip Maffettone, Emily Delaney, Peyton Greenside, and Andrew Gordon Wilson. arXiv, July 12, 2022. http://arxiv.org/abs/2203.12742. samuelstanton/lambo

Classes

FoldxInterface(working_dir[, verbose])

A class for interacting with FoldX, a protein engineering software.