ArticleProtein science : a publication of the Protein Society2025
Applicability of AlphaFold2 in the modeling of dimeric, trimeric, and tetrameric coiled-coil domains.
Article in Protein science : a publication of the Protein Society, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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13 citing papers in PubMed.
- Integrative structural modelling reveals the human Mic60-Mic19 subcomplex as a diffusion barrier in mitochondria.Nature communications · 2026Article
- Conformational diversity in poly-HAMP arrays and its implications for signal transduction.Protein science : a publication of the Protein Society · 2026Article
- From Thanatos to transcription: the emerging biology of THAP proteins.Cellular and molecular life sciences : CMLS · 2026Review
- Fusion protein condensate formation via coiled-coil domains.Protein science : a publication of the Protein Society · 2026Article
- When can AlphaFold predict the oligomeric states of proteins?Protein science : a publication of the Protein Society · 2026Article
- Computational prediction resolves thousands of homooligomeric phage protein structures.bioRxiv : the preprint server for biology · 2026Article
- Bromodomain dimers: A case study of BRD4 and family-wide AlphaFold predictions.Structural dynamics (Melville, N.Y.) · 2026Article
- Sequence Prediction, Structural Modelling and the Challenges of Plasticity in Coiled Coils.Sub-cellular biochemistry · 2026Review
- De Novo Design of Parallel and Antiparallel ABiochemistry · 2025Article
- Assessment of the Topology and Oligomerisation States of Coiled Coils Using Metadynamics with Conformational Restraints.Journal of chemical theory and computation · 2025Article
- AlphaFold 2, but not AlphaFold 3, predicts confident but unrealistic β-solenoid structures for repeat proteins.Computational and structural biotechnology journal · 2025Article
- CCfrag: scanning folding potential of coiled-coil fragments with AlphaFold.Bioinformatics advances · 2025Article
- Applicability of AlphaFold2 in the modeling of dimeric, trimeric, and tetrameric coiled-coil domains.Protein science : a publication of the Protein Society · 2025Article
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5 authors.
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Abstract
Coiled coils are a common protein structural motif involved in cellular functions ranging from mediating protein-protein interactions to facilitating processes such as signal transduction or regulation of gene expression. They are formed by two or more alpha helices that wind around a central axis to form a buried hydrophobic core. Various forms of coiled-coil bundles have been reported, each characterized by the number, orientation, and degree of winding of the constituent helices. This variability is underpinned by short sequence repeats that form coiled coils and whose properties determine both their overall topology and the local geometry of the hydrophobic core. The strikingly repetitive sequence has enabled the development of accurate sequence-based coiled-coil prediction methods; however, the modeling of coiled-coil domains remains a challenging task. In this work, we evaluated the accuracy of AlphaFold2 in modeling coiled-coil domains, both in modeling local geometry and in predicting global topological properties. Furthermore, we show that the prediction of the oligomeric state of coiled-coil bundles can be achieved by using the internal representations of AlphaFold2, with a performance better than any previous state-of-the-art method (code available at https://github.com/labstructbioinf/dc2_oligo).
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