SPAED: harnessing AlphaFold output for accurate segmentation of phage endolysin domains.

ABSTRACT:

Summary

SPAED is an accessible tool for the accurate segmentation of protein domains that leverages information contained in the predicted aligned error (PAE) matrix obtained from AlphaFold to better identify domain-linker boundaries and detect terminal disordered regions. On a dataset of 376 bacteriophage endolysins (proteins that degrade the bacterial cell wall), SPAED achieves a mean intersect-over-union score of 96% and a domain-boundary-distance score of 89% compared to 94% and 70%, respectively, for the state-of-the-art tool Chainsaw.

Availability and implementation

Implemented in Python, SPAED is accessible on the web (https://spaed.ca) and available for download from https://github.com/Rousseau-Team/spaed or https://pypi.org/project/spaed. The data used to test SPAED

SUBMITTER: Boulay A 

PROVIDER: S-EPMC12518921 | biostudies-literature | 2025 Oct

REPOSITORIES: biostudies-literature