ArticleNature communications2023
Accurate prediction of protein assembly structure by combining AlphaFold and symmetrical docking.
Article in Nature communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Virtual cell: Current perspectives and future prospects.The Journal of international medical research · 2026Review
- Multiplex gene editing drives revolution in crop breeding: overlaid editing of multiple genes and customization of complex traits.Advanced biotechnology · 2026Review
- From CASP13 to the Nobel Prize: DeepMind's AlphaFold Journey in Revolutionizing Protein Structure Prediction and Beyond.Current protein & peptide science · 2026Review
- StoPred: Accurate Stoichiometry Prediction for Protein Complexes Using Protein Language Models and Graph Attention.Research square · 2025Article
- StoPred: Accurate Stoichiometry Prediction for Protein Complexes Using Protein Language Models and Graph Attention.bioRxiv : the preprint server for biology · 2025Article
- Investigating whether deep learning models for co-folding learn the physics of protein-ligand interactions.Nature communications · 2025Article
- Positive selection at core genes may underlie niche adaptation in Fusobacterium animalis.Gut pathogens · 2025Article
- Identification of gut bacteria reductases that biotransform steroid hormones.Nature communications · 2025Article
- Recent progress and future challenges in structure-based protein-protein interaction prediction.Molecular therapy : the journal of the American Society of Gene Therapy · 2025Review
- Predictomes, a classifier-curated database of AlphaFold-modeled protein-protein interactions.Molecular cell · 2025Article
- Multimeric protein interaction and complex prediction: Structure, dynamics and function.Computational and structural biotechnology journal · 2025Review
- Cognitive Impact of Neurotropic Pathogens: Investigating Molecular Mimicry through Computational Methods.Cellular and molecular neurobiology · 2024Article
- SymProFold: Structural prediction of symmetrical biological assemblies.Nature communications · 2024Article
- The power and pitfalls of AlphaFold2 for structure prediction beyond rigid globular proteins.Nature chemical biology · 2024Review
- [A look into the neighboring discipline: eHealth in oncology].Chirurgie (Heidelberg, Germany) · 2024Review
- Predictomes: A classifier-curated database of AlphaFold-modeled protein-protein interactions.bioRxiv : the preprint server for biology · 2024Article
- From cancer therapy to cardiac safety: the role of proteostasis in drug-induced cardiotoxicity.Frontiers in pharmacology · 2024Review
- Accurate prediction of protein assembly structure by combining AlphaFold and symmetrical docking.Nature communications · 2023Article
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2 authors.
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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, 27 cubic systems were assembled with a median TM-score of 0.99 and a DockQ score of 0.72. 21 had TM-scores of above 0.9 and were categorized as acceptable- to 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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