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Using AlphaFold Multimer to discover interkingdom protein-protein interactions
Open accessPreprint — published as 10.1111/tpj.16969 · Paper page
Abstract
Structural prediction by artificial intelligence (AI) can be powerful new instruments to discover novel protein-protein interactions, but the community still grapples with the implementation, opportunities and limitations. Here, we discuss and re-analyse our in-silico screen for novel pathogen-secreted inhibitors of immune hydrolases to illustrate the power and limitations of structural predictions. We discuss strategies of curating sequences, including controls, and reusing sequence alignments and highlight important limitations originating from platforms, sequence depth and computing times. We hope these experiences will support similar interactomic screens by the research community.
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Citations
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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Research works printed but not linked: 28
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Metadata
- Authors
- Homma, F., Lyu, J., & van der Hoorn, R. A. L.
- Affiliations
- University of Oxford (GB)
- Corresponding author
- van der Hoorn, Renier A. L.
- Venue
- The Plant Journal
- Publisher
- openRxiv
- Published
- 2024-06-14
- Volume
- 120
- Issue
- 1
- Pages
- 19-28
- ISSN
- 0960-7412 (ISSN-L)
- OpenAlex
- W4401667289
- Cited by
- 37
- References
- 1
- Citations by year
- 2026: 15 · 2025: 19 · 2024: 3
- FWCI
- 5.04
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- cc-by
- Locations
- The Plant Journal (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
- PubMed (publishedVersion)
- Funders
- University of Oxford
- Biotechnology and Biological Sciences Research Council (DDT00230, 101019324)
- European Research Council (101019324)
- 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 › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
- Keywords
- AlphaFold-Multimer, protein-protein interaction, cross-kingdom interactions, sequence curation, plant-pathogen interaction
- MeSH terms
- Artificial Intelligence, Plant Proteins, Sequence Alignment, Protein Interaction Mapping
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