SPAED: harnessing AlphaFold output for accurate segmentation of phage endolysin domains
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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 can be found at https://doi.org/10.5281/zenodo.15285860.
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Cites
Highly accurate protein structure prediction with AlphaFold
Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Žídek, A., Potapenko, A., et al. (2021) · Nature · doi:10.1038/s41586-021-03819-2 · Cited by 43,764 · see citing works
Accurate structure prediction of biomolecular interactions with AlphaFold 3
Abramson, J., Adler, J., Dunger, J., Evans, R., Green, T., Pritzel, A., Ronneberger, O., Willmore, L., Ballard, A. J., Bambrick, J., et al. (2024) · Nature · doi:10.1038/s41586-024-07487-w · Cited by 15,861 · see citing works
De novo design of protein structure and function with RFdiffusion
Watson, J. L., Juergens, D., Bennett, N. R., Trippe, B. L., Yim, J., Eisenach, H. E., Ahern, W., Borst, A. J., Ragotte, R. J., Milles, L. F., et al. (2023) · Nature · doi:10.1038/s41586-023-06415-8 · Cited by 2,325 · see citing works
Chainsaw: protein domain segmentation with fully convolutional neural networks
Wells, J., Hawkins-Hooker, A., Bordin, N., Sillitoe, I., Paige, B., & Orengo, C. (2023) · doi:10.1101/2023.07.19.549732 · Cited by 53 · see citing works
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- Authors
- Boulay, A., Cremelie, E., Galiez, C., Briers, Y., Rousseau, E., & Vázquez, R.
- Affiliations
- Ghent University (BE)
- Institut polytechnique de Grenoble (FR)
- Université Laval (CA)
- Corresponding author
- Rousseau, Elsa
- Vázquez, Roberto
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2025-09-24
- Volume
- 41
- Issue
- 10
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- PMC
- PMC12518921
- OpenAlex
- W4414458008
- Cited by
- 4
- References
- 4
- Citations by year
- 2026: 4
- FWCI
- 1.19
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Bioinformatics (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nd)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Ghent University Academic Bibliography (Ghent University) (submittedVersion, cc-by)
- Funders
- Fonds de recherche du Québec secteur Nature et technologies (325947)
- CREATE Responsible Health and Healthcare Data Science
- Natural Sciences and Engineering Research Council of Canada
- Mitacs Globalink Research program (IT41138)
- Research Scholars—Junior 1
- Fonds de recherche du Québec secteur Santé (307935)
- Bijzonder Onderzoeksfonds (01P10022)
- 2024 from the European Society of Clinical Microbiology and Infectious Diseases
- Research Foundation—Flanders (1S15424N)
- Compute Ontario
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Machine Learning in Bioinformatics
- Physical Sciences › Environmental Science › Ecology › Bacteriophages and microbial interactions
- Keywords
- endolysin, AlphaFold, intrinsically disordered regions, protein structure prediction
- MeSH terms
- Protein Domains, Bacteriophages, Endopeptidases, Software, Viral Proteins, Computational Biology
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