ArticleBioinformatics (Oxford, England)2021
A library of coiled-coil domains: from regular bundles to peculiar twists.
Article in Bioinformatics (Oxford, England), 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- Conformational diversity in poly-HAMP arrays and its implications for signal transduction.Protein science : a publication of the Protein Society · 2026Article
- Coiled-coil homo-oligomerization and disaggregase Hsp104 act in parallel to stabilize orphan septins.bioRxiv : the preprint server for biology · 2026Article
- Heptad insertion extends theBiodesign research · 2026Article
- Fibril Structure of Desiccation-Protective Tardigrade Protein CAHS-8.Angewandte Chemie (International ed. in English) · 2026Article
- Investigating the role of EFhd2 protein in modulating tau pathology in a tauopathy mouse model.Frontiers in molecular neuroscience · 2026Article
- Sequence Prediction, Structural Modelling and the Challenges of Plasticity in Coiled Coils.Sub-cellular biochemistry · 2026Review
- Coil-Tag Conjugation: A Next Gen Site-Specific ADC Fabrication Technology.Bioconjugate insights · 2026Article
- Metallo-coiled Coil Stabilization via Chemical Cross-Linking: Implications for Gd(III)-Based MRI Contrast Agents.Journal of the American Chemical Society · 2025Article
- COMP Is a Biomarker of Cartilage Destruction, Extracellular Matrix and Vascular Remodeling and Tissue Repair.International journal of molecular sciences · 2025Review
- Insights Into the Conformational Dynamics of the Cytoplasmic Domain of Metal-Sensing Sensor Histidine Kinase ZraS.Proteins · 2025Article
- Applicability of AlphaFold2 in the modeling of dimeric, trimeric, and tetrameric coiled-coil domains.Protein science : a publication of the Protein Society · 2025Article
- The structural logic of dynamic signaling in the Escherichia coli serine chemoreceptor.Protein science : a publication of the Protein Society · 2024Article
- The Structural Logic of Dynamic Signaling in thebioRxiv : the preprint server for biology · 2024Article
- CoCoNat: A Deep Learning-Based Tool for the Prediction of Coiled-coil Domains in Protein Sequences.Bio-protocol · 2024Article
- AlphaFold2 captures the conformational landscape of the HAMP signaling domain.Protein science : a publication of the Protein Society · 2024Article
- CCProtein science : a publication of the Protein Society · 2023Article
- X-ray structure of the metastable SEPT14-SEPT7 coiled coil reveals a hendecad region crucial for heterodimerization.Acta crystallographica. Section D, Structural biology · 2023Article
- CoCoNat: a novel method based on deep learning for coiled-coil prediction.Bioinformatics (Oxford, England) · 2023Article
- From primordial clocks to circadian oscillators.Nature · 2023Article
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Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
motivationCoiled coils are widespread protein domains involved in diverse processes ranging from providing structural rigidity to the transduction of conformational changes. They comprise two or more α-helices that are wound around each other to form a regular supercoiled bundle. Owing to this regularity, coiled-coil structures can be described with parametric equations, thus enabling the numerical representation of their properties, such as the degree and handedness of supercoiling, rotational state of the helices, and the offset between them. These descriptors are invaluable in understanding the function of coiled coils and designing new structures of this type. The existing tools for such calculations require manual preparation of input and are therefore not suitable for the high-throughput analyses.
resultsTo address this problem, we developed SamCC-Turbo, a software for fully automated, per-residue measurement of coiled coils. By surveying Protein Data Bank with SamCC-Turbo, we generated a comprehensive atlas of ∼50 000 coiled-coil regions. This machine learning-ready dataset features precise measurements as well as decomposes coiled-coil structures into fragments characterized by various degrees of supercoiling. The potential applications of SamCC-Turbo are exemplified by analyses in which we reveal general structural features of coiled coils involved in functions requiring conformational plasticity. Finally, we discuss further directions in the prediction and modeling of coiled coils. AVAILABILITY AND IMPLEMENTATION: SamCC-Turbo is available as a web server (https://lbs.cent.uw.edu.pl/samcc_turbo) and as a Python library (https://github.com/labstructbioinf/samcc_turbo), whereas the results of the Protein Data Bank scan can be browsed and downloaded at https://lbs.cent.uw.edu.pl/ccdb. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.