Related Experiment Video
Updated: Jan 6, 2026
Interactome-Seq: A Protocol for Domainome Library Construction, Validation and Selection by Phage Display and Next Generation Sequencing
Published on: October 3, 2018
SPAED: harnessing AlphaFold output for accurate segmentation of phage endolysin domains
Alexandre Boulay1,2,3, Emma Cremelie1, Clovis Galiez4
1Department of Biotechnology, Ghent University, Ghent B-9000, Belgium.
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 can be found at https://doi.org/10.5281/zenodo.15285860.
