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SPAED: Harnessing AlphaFold Output for Accurate Segmentation of Phage Endolysin Domains
Open accessPreprint — published as 10.1093/bioinformatics/btaf531 · Paper page
Abstract
Summary: SPAED is an accessible tool for the accurate segmentation of protein domains that applies hierarchical clustering to the predicted aligned error (PAE) matrix obtained from AlphaFold predictions. It leverages information contained in the PAE matrix to better identify domain-linker boundaries and detect 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: SPAED is available on the web at http://spaed.ca and available for download at https://github.com/Rousseau-Team/spaed . Contact: Elsa Rousseau - elsa.rousseau@ift.ulaval.ca , Roberto Vázquez - rvazqf@gmail.com
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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
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Metadata
- 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
- openRxiv
- Published
- 2025-04-28
- Volume
- 41
- Issue
- 10
- ISSN
- 1367-4803 (ISSN-L)
- PMC
- PMC12518921
- OpenAlex
- W4414458008
- Cited by
- 4
- References
- 1
- Citations by year
- 2026: 4
- FWCI
- 1.20
- 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
- European Society of Clinical Microbiology and Infectious Diseases
- Fonds Wetenschappelijk Onderzoek (1S15424N)
- Universiteit Gent (01P10022)
- Mitacs
- Vlaamse regering
- Alliance de recherche numérique du Canada
- Natural Sciences and Engineering Research Council of Canada
- Fonds de Recherche du Québec - Santé (307935, Junior 1)
- Fonds de recherche du Québec – Nature et technologies (325947)
- 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
- Life Sciences › Immunology and Microbiology › Virology › 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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