ArticleProtein science : a publication of the Protein Society2018
CCBuilder 2.0: Powerful and accessible coiled-coil modeling.
Article in Protein science : a publication of the Protein Society, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 78 papers.
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Who cites it
78 citing papers in PubMed, 134 citations in OpenAlex.
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- InsiliCoil: An Integrated Software Suite for Coiled Coil Design, Prediction, and Therapeutic Engineering.ACS synthetic biology · 2026Article
- Sequence Prediction, Structural Modelling and the Challenges of Plasticity in Coiled Coils.Sub-cellular biochemistry · 2026Review
- Designability of α-Helical Protein Filaments.Sub-cellular biochemistry · 2026Review
- Dimeric Cin8 motors have an inherent plus-end bias and weak inter-head coordination.bioRxiv : the preprint server for biology · 2025Article
- Deep learning-assisted tools to understand the structural biology of the synapse.Biomedical engineering letters · 2025Review
- Fabrication of cytotoxic mirror image nanopores.Nature communications · 2025Article
- Dynamic ensembles of SARS-CoV-2 N-protein reveal head-to-head coiled-coil-driven oligomerization and phase separation.Nucleic acids research · 2025Article
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- Proteomimetic Strategy for the Modulation of Intrinsically Disordered Protein MYC.Journal of the American Chemical Society · 2025Article
- Digital and Tunable Genetically Encoded Tension Sensors Based on Engineered Coiled-Coils.Angewandte Chemie (International ed. in English) · 2025Article
- Exploring Shootin1's oncogenic role withinTurkish journal of biology = Turk biyoloji dergisi · 2025Article
- Applicability of AlphaFold2 in the modeling of dimeric, trimeric, and tetrameric coiled-coil domains.Protein science : a publication of the Protein Society · 2025Article
- Structural basis for surface activation of the classical complement cascade by the short pentraxin C-reactive protein.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
18 more citing papers are in PubMed but not listed here.
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2 authors at 1 institution in 1 country.
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Abstract
The increased availability of user-friendly and accessible computational tools for biomolecular modeling would expand the reach and application of biomolecular engineering and design. For protein modeling, one key challenge is to reduce the complexities of 3D protein folds to sets of parametric equations that nonetheless capture the salient features of these structures accurately. At present, this is possible for a subset of proteins, namely, repeat proteins. The α-helical coiled coil provides one such example, which represents ≈ 3-5% of all known protein-encoding regions of DNA. Coiled coils are bundles of α helices that can be described by a small set of structural parameters. Here we describe how this parametric description can be implemented in an easy-to-use web application, called CCBuilder 2.0, for modeling and optimizing both α-helical coiled coils and polyproline-based collagen triple helices. This has many applications from providing models to aid molecular replacement for X-ray crystallography, in silico model building and engineering of natural and designed protein assemblies, and through to the creation of completely de novo "dark matter" protein structures. CCBuilder 2.0 is available as a web-based application, the code for which is open-source and can be downloaded freely. http://coiledcoils.chm.bris.ac.uk/ccbuilder2. LAY SUMMARY: We have created CCBuilder 2.0, an easy to use web-based application that can model structures for a whole class of proteins, the α-helical coiled coil, which is estimated to account for 3-5% of all proteins in nature. CCBuilder 2.0 will be of use to a large number of protein scientists engaged in fundamental studies, such as protein structure determination, through to more-applied research including designing and engineering novel proteins that have potential applications in biotechnology.
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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.