SPAED: harnessing AlphaFold output for accurate segmentation of phage endolysin domains.
basic_science · Level V
Where this comes from
- Record sourced from PubMed, PMID 40991341.
- Also identified by DOI 10.1093/bioinformatics/btaf531 and PMC identifier 12518921.
- Licence recorded as CC BY.
- The licence permits redistribution, so the abstract is shown in full and the full text is available from the publisher.
Abstract
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. 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.
Medical subject headings
- Endopeptidases
- Software
- Bacteriophages
- Viral Proteins
- Computational Biology