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gapTrick – Structural characterisation of protein-protein interactions using AlphaFold
Open accessPreprint — published as 10.1093/bioinformatics/btaf532
Abstract
The structural characterisation of protein-protein interactions is a key step in understanding the functions of living cells. Here I show that AlphaFold3 often fails to predict protein complexes that are either weak, or dependent on the presence of a cofactor that is not included in a prediction. To address this problem, I developed gapTrick, an AlphaFold2-based approach that uses multimeric templates to improve prediction reliability. I show that gapTrick improves predictions of weak and incomplete complexes based on low-accuracy templates, such as separate protein models rigid-body fitted into a cryo-EM reconstruction. I also show that it identifies with very high precision residue-residue interactions, which are critical for complex formation and a very strong indicator of model correctness. The approach can aid in the interpretation of challenging experimental structures and the computational identification of protein-protein interactions. Availability and implementation: The gapTrick source code is available at https://github.com/gchojnowski/gapTrick and requires only a standard AlphaFold2 installation to run. The repository also provides a Colab notebook that can be used to run gapTrick without installing it on the user’s computer.
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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
- Chojnowski, G.
- Affiliations
- European Molecular Biology Laboratory (DE)
- Corresponding author
- Chojnowski, Grzegorz
- ORCID
- Chojnowski, Grzegorz
- Venue
- Bioinformatics
- Publisher
- openRxiv
- Published
- 2025-02-05
- Volume
- 41
- Issue
- 9
- ISSN
- 1367-4803 (ISSN-L)
- PMC
- PMC12479393
- OpenAlex
- W4414436051
- Cited by
- 3
- References
- 1
- Citations by year
- 2026: 3
- FWCI
- 0.90
- 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)
- PubMed Central (publishedVersion, cc-by)
- Funders
- European Molecular Biology Laboratory
- 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
- protein-protein interaction, protein complex structure prediction, AlphaFold2, AlphaFold3, cryo-EM reconstruction, residue-residue interactions, template-based modeling
- MeSH terms
- Models, Molecular, Protein Binding, Protein Conformation, Proteins, Software, Computational Biology, Cryoelectron Microscopy, Protein Interaction Mapping
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