ArticleBioinformatics (Oxford, England)2023
CoCoNat: a novel method based on deep learning for coiled-coil prediction.
Article in Bioinformatics (Oxford, England), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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21 citing papers in PubMed.
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- Heterotrimeric kinesin-2 autoinhibition mediated by interactions of the CC2 and proximal tail domains with the motor domains is essential for cilium formation and maintenance.bioRxiv : the preprint server for biology · 2026Article
- AlphaFold-driven discovery of oxysterol-binding protein-related protein-phosphoinositide 3-, 4-, and 5-phosphatase interactions using new generation confidence scores.Protein science : a publication of the Protein Society · 2026Article
- The C16orf87 protein is a subunit of the MIER corepressor complex controlling embryonic development and cell migration.Scientific reports · 2026Article
- Dimeric Cin8 motors have an inherent plus-end bias and weak interhead coordination.Biophysical journal · 2026Article
- Phased potato genome assembly and association genetics enable delineation of the H1 resistance locus against potato cyst nematodes.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- Article
- A dramatic protein fold switch powers a bactericidal nanomachine.bioRxiv : the preprint server for biology · 2026Article
- Sequence Prediction, Structural Modelling and the Challenges of Plasticity in Coiled Coils.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
- Acyl-CoA-binding protein AcbdA is required for peroxisome hitchhiking on early endosomes inMolecular biology of the cell · 2025Article
- Conformational plasticity of disordered regions enables sequence-diverse DNA recognition by transcription factor AflR.Nature communications · 2025Article
- Assessment of the Topology and Oligomerisation States of Coiled Coils Using Metadynamics with Conformational Restraints.Journal of chemical theory and computation · 2025Article
- Applicability of AlphaFold2 in the modeling of dimeric, trimeric, and tetrameric coiled-coil domains.Protein science : a publication of the Protein Society · 2025Article
- Dynamic pre-structuration of lipid nanodomain-segregating remorin proteins.Communications biology · 2024Article
- The success rate of processed predicted models in molecular replacement: implications for experimental phasing in the AlphaFold era.Acta crystallographica. Section D, Structural biology · 2024Article
- Molecular dissection of the chromosome partitioning protein RocS and regulation by phosphorylation.Journal of bacteriology · 2024Article
- Increased susceptibility to Mycobacterium avium complex infection in miniature Schnauzer dogs caused by a codon deletion in CARD9.Scientific reports · 2024Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationCoiled-coil domains (CCD) are widespread in all organisms and perform several crucial functions. Given their relevance, the computational detection of CCD is very important for protein functional annotation. State-of-the-art prediction methods include the precise identification of CCD boundaries, the annotation of the typical heptad repeat pattern along the coiled-coil helices as well as the prediction of the oligomerization state.
resultsIn this article, we describe CoCoNat, a novel method for predicting coiled-coil helix boundaries, residue-level register annotation, and oligomerization state. Our method encodes sequences with the combination of two state-of-the-art protein language models and implements a three-step deep learning procedure concatenated with a Grammatical-Restrained Hidden Conditional Random Field for CCD identification and refinement. A final neural network predicts the oligomerization state. When tested on a blind test set routinely adopted, CoCoNat obtains a performance superior to the current state-of-the-art both for residue-level and segment-level CCD. CoCoNat significantly outperforms the most recent state-of-the-art methods on register annotation and prediction of oligomerization states. AVAILABILITY AND IMPLEMENTATION: CoCoNat web server is available at https://coconat.biocomp.unibo.it. Standalone version is available on GitHub at https://github.com/BolognaBiocomp/coconat.
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