DepoScope : accurate phage depolymerase annotation and domain delineation using large language models
- Author
- Robby Concha-Eloko, Michiel Stock (UGent) , Bernard De Baets (UGent) , Yves Briers (UGent) , Rafael Sanjuán, Pilar Domingo-Calap and Dimitri Boeckaerts
- Organization
- Project
- Abstract
- Bacteriophages (phages) are viruses that infect bacteria. Many of them produce specific enzymes called depolymerases to break down external polysaccharide structures. Accurate annotation and domain identification of these depolymerases are challenging due to their inherent sequence diversity. Hence, we present DepoScope, a machine learning tool that combines a fine-tuned ESM-2 model with a convolutional neural network to identify depolymerase sequences and their enzymatic domains precisely. To accomplish this, we curated a dataset from the INPHARED phage genome database, created a polysaccharide-degrading domain database, and applied sequential filters to construct a high-quality dataset, which is subsequently used to train DepoScope. Our work is the first approach that combines sequence-level predictions with amino-acid-level predictions for accurate depolymerase detection and functional domain identification. In that way, we believe that DepoScope can greatly enhance our understanding of phage-host interactions at the level of depolymerases.
- Keywords
- PROTEIN, INSIGHTS
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Citation
Please use this url to cite or link to this publication: http://hdl.handle.net/1854/LU-01J5MNHRKRMQFSVFWFK7EBP2WF
- MLA
- Concha-Eloko, Robby, et al. “DepoScope : Accurate Phage Depolymerase Annotation and Domain Delineation Using Large Language Models.” PLOS COMPUTATIONAL BIOLOGY, vol. 20, no. 8, 2024, doi:10.1371/journal.pcbi.1011831.
- APA
- Concha-Eloko, R., Stock, M., De Baets, B., Briers, Y., Sanjuán, R., Domingo-Calap, P., & Boeckaerts, D. (2024). DepoScope : accurate phage depolymerase annotation and domain delineation using large language models. PLOS COMPUTATIONAL BIOLOGY, 20(8). https://doi.org/10.1371/journal.pcbi.1011831
- Chicago author-date
- Concha-Eloko, Robby, Michiel Stock, Bernard De Baets, Yves Briers, Rafael Sanjuán, Pilar Domingo-Calap, and Dimitri Boeckaerts. 2024. “DepoScope : Accurate Phage Depolymerase Annotation and Domain Delineation Using Large Language Models.” PLOS COMPUTATIONAL BIOLOGY 20 (8). https://doi.org/10.1371/journal.pcbi.1011831.
- Chicago author-date (all authors)
- Concha-Eloko, Robby, Michiel Stock, Bernard De Baets, Yves Briers, Rafael Sanjuán, Pilar Domingo-Calap, and Dimitri Boeckaerts. 2024. “DepoScope : Accurate Phage Depolymerase Annotation and Domain Delineation Using Large Language Models.” PLOS COMPUTATIONAL BIOLOGY 20 (8). doi:10.1371/journal.pcbi.1011831.
- Vancouver
- 1.Concha-Eloko R, Stock M, De Baets B, Briers Y, Sanjuán R, Domingo-Calap P, et al. DepoScope : accurate phage depolymerase annotation and domain delineation using large language models. PLOS COMPUTATIONAL BIOLOGY. 2024;20(8).
- IEEE
- [1]R. Concha-Eloko et al., “DepoScope : accurate phage depolymerase annotation and domain delineation using large language models,” PLOS COMPUTATIONAL BIOLOGY, vol. 20, no. 8, 2024.
@article{01J5MNHRKRMQFSVFWFK7EBP2WF,
abstract = {{Bacteriophages (phages) are viruses that infect bacteria. Many of them produce specific enzymes called depolymerases to break down external polysaccharide structures. Accurate annotation and domain identification of these depolymerases are challenging due to their inherent sequence diversity. Hence, we present DepoScope, a machine learning tool that combines a fine-tuned ESM-2 model with a convolutional neural network to identify depolymerase sequences and their enzymatic domains precisely. To accomplish this, we curated a dataset from the INPHARED phage genome database, created a polysaccharide-degrading domain database, and applied sequential filters to construct a high-quality dataset, which is subsequently used to train DepoScope. Our work is the first approach that combines sequence-level predictions with amino-acid-level predictions for accurate depolymerase detection and functional domain identification. In that way, we believe that DepoScope can greatly enhance our understanding of phage-host interactions at the level of depolymerases.}},
articleno = {{e1011831}},
author = {{Concha-Eloko, Robby and Stock, Michiel and De Baets, Bernard and Briers, Yves and Sanjuán, Rafael and Domingo-Calap, Pilar and Boeckaerts, Dimitri}},
issn = {{1553-734X}},
journal = {{PLOS COMPUTATIONAL BIOLOGY}},
keywords = {{PROTEIN,INSIGHTS}},
language = {{eng}},
number = {{8}},
pages = {{15}},
title = {{DepoScope : accurate phage depolymerase annotation and domain delineation using large language models}},
url = {{http://doi.org/10.1371/journal.pcbi.1011831}},
volume = {{20}},
year = {{2024}},
}
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