Using AlphaFold Multimer to discover interkingdom protein–protein interactions
Open accessPublished version of a preprint
Abstract
SUMMARY: Structural prediction by artificial intelligence 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 caused by different platforms, sequence depth and computing times. We hope these experiences will support similar interactomic screens by the research community.
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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
ColabFold - Making protein folding accessible to all
Mirdita, M., Schütze, K., Moriwaki, Y., Heo, L., Ovchinnikov, S., & Steinegger, M. (2021) · doi:10.1101/2021.08.15.456425 · Cited by 9,391 · see citing works
Protein complex prediction with AlphaFold-Multimer
Evans, R., O’Neill, M., Pritzel, A., Antropova, N., Senior, A., Green, T., Žídek, A., Bates, R., Blackwell, S., Yim, J., et al. (2021) · doi:10.1101/2021.10.04.463034 · Cited by 3,808 · see citing works
Improved prediction of protein-protein interactions using AlphaFold2
Bryant, P., Pozzati, G., & Elofsson, A. (2021) · doi:10.1101/2021.09.15.460468 · Cited by 1,025 · see citing works
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- Authors
- Homma, F., Lyu, J., & van der Hoorn, R. A. L.
- Affiliations
- University of Oxford (GB)
- The Plant Chemetics Laboratory, Department of Biology University of Oxford OX1 3RB Oxford UK
- Venue
- The Plant Journal
- Publisher
- Wiley
- Published
- 2024-08-17
- Volume
- 120
- Issue
- 1
- Pages
- 19-28
- ISSN
- 0960-7412 (ISSN-L)
- 1365-313X
- OpenAlex
- W4401667289
- Cited by
- 37
- References
- 5
- Citations by year
- 2026: 15 · 2025: 19 · 2024: 3
- FWCI
- 5.02
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- The Plant Journal (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
- PubMed (publishedVersion)
- Funders
- European Research Council (101019324)
- Biotechnology and Biological Sciences Research Council (DDT00230)
- 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 › Materials Science › Materials Chemistry › 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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