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Accurate prediction of protein assembly structure by combining AlphaFold and symmetrical docking
Open accessPreprint — published as 10.1038/s41467-023-43681-6 · Paper page
Abstract
AlphaFold can predict the structures of monomeric and multimeric proteins with high accuracy but has a limit on the number of chains and residues it can fold. Here we show that a combination of AlphaFold and all-atom symmetric docking simulations enables highly accurate prediction of the structure of complex symmetrical assemblies. We present a method to predict the structure of complexes with cubic – tetrahedral, octahedral and icosahedral – symmetry from sequence. Focusing on proteins where AlphaFold can make confident predictions on the subunit structure, 21 cubic systems were assembled with a median TM-score of 0.99 and a DockQ score of 0.71. 15 had TM-scores of above 0.8 and were categorized as high-quality according to DockQ. The resulting models are energetically optimized and can be used for detailed studies of intermolecular interactions in higher-order symmetrical assemblies. The results demonstrate how explicit treatment of structural symmetry can significantly expand the size and complexity of AlphaFold predictions.
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Highly accurate protein structure prediction with AlphaFold
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Metadata
- Authors
- Jeppesen, M., & André, I.
- Affiliations
- Lund University (SE)
- Corresponding author
- André, Ingemar
- Venue
- Nature Communications
- Publisher
- openRxiv
- Published
- 2023-06-24
- Volume
- 14
- Issue
- 1
- Pages
- 8283-8283
- ISSN
- 2041-1723 (ISSN-L)
- PMC
- PMC10719378
- OpenAlex
- W4389686140
- Cited by
- 44
- References
- 1
- Citations by year
- 2026: 13 · 2025: 17 · 2024: 13 · 2023: 1
- FWCI
- 3.92
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- cc-by
- Locations
- Nature Communications (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nd)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Lund University Publications (Lund University) (submittedVersion)
- Funders
- European Commission (HORIZON2020, 771820)
- Lunds Universitet
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
- Life Sciences › Pharmacology, Toxicology and Pharmaceutics › Drug Discovery › Computational Drug Discovery Methods
- Keywords
- AlphaFold, cubic symmetry, tetrahedral symmetry, octahedral symmetry, icosahedral symmetry, structural symmetry, multimeric proteins, TM-score, intermolecular interactions
- MeSH terms
- Protein Conformation, Proteins
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