ArticlePloS one2011
Multicoil2: predicting coiled coils and their oligomerization states from sequence in the twilight zone.
Article in PloS one, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 55 papers.
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Who cites it
55 citing papers in PubMed.
- The C16orf87 protein is a subunit of the MIER corepressor complex controlling embryonic development and cell migration.Scientific reports · 2026Article
- Sequence Prediction, Structural Modelling and the Challenges of Plasticity in Coiled Coils.Sub-cellular biochemistry · 2026Review
- TRAF6 coiled-coil domain mediates its trimerization.bioRxiv : the preprint server for biology · 2025Article
- SCEP3 initiates synapsis and implements crossover interference in Arabidopsis.Nature plants · 2025Article
- Exploration of the interaction between dynein intermediate chain and dynactin p150Protein science : a publication of the Protein Society · 2025Article
- Assessment of the Topology and Oligomerisation States of Coiled Coils Using Metadynamics with Conformational Restraints.Journal of chemical theory and computation · 2025Article
- Beyond Static Tethering at Membrane Contact Sites: Structural Dynamics and Functional Implications of VAP Proteins.Molecules (Basel, Switzerland) · 2025Review
- Plant-specific tail-anchored coiled-coil protein MAG3 stabilizes Golgi-associated ERESs to facilitate protein exit from the ER.Communications biology · 2025Article
- Divergence in expression of a singing-related neuroplasticity gene in the brains of 2 Ficedula flycatchers and their hybrids.G3 (Bethesda, Md.) · 2025Article
- Recent Advances in Computational Prediction of Secondary and Supersecondary Structures from Protein Sequences.Methods in molecular biology (Clifton, N.J.) · 2025Review
- Dynamic pre-structuration of lipid nanodomain-segregating remorin proteins.Communications biology · 2024Article
- Article
- CoCoNat: a novel method based on deep learning for coiled-coil prediction.Bioinformatics (Oxford, England) · 2023Article
- Intrinsic mesoscale properties of a Polycomb protein underpin heterochromatin fidelity.Nature structural & molecular biology · 2023Article
- CERT1 mutations perturb human development by disrupting sphingolipid homeostasis.The Journal of clinical investigation · 2023Article
- NDP52 acts as a redox sensor in PINK1/Parkin-mediated mitophagy.The EMBO journal · 2023Article
- Oncogenic driver FGFR3-TACC3 requires five coiled-coil heptads for activation and disulfide bond formation for stability.Oncotarget · 2023Article
- Protein Design: From the Aspect of Water Solubility and Stability.Chemical reviews · 2022Review
- Article
- Dimerization-dependent membrane tethering by Atg23 is essential for yeast autophagy.Cell reports · 2022Article
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4 authors.
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Abstract
The alpha-helical coiled coil can adopt a variety of topologies, among the most common of which are parallel and antiparallel dimers and trimers. We present Multicoil2, an algorithm that predicts both the location and oligomerization state (two versus three helices) of coiled coils in protein sequences. Multicoil2 combines the pairwise correlations of the previous Multicoil method with the flexibility of Hidden Markov Models (HMMs) in a Markov Random Field (MRF). The resulting algorithm integrates sequence features, including pairwise interactions, through multinomial logistic regression to devise an optimized scoring function for distinguishing dimer, trimer and non-coiled-coil oligomerization states; this scoring function is used to produce Markov Random Field potentials that incorporate pairwise correlations localized in sequence. Multicoil2 significantly improves both coiled-coil detection and dimer versus trimer state prediction over the original Multicoil algorithm retrained on a newly-constructed database of coiled-coil sequences. The new database, comprised of 2,105 sequences containing 124,088 residues, includes reliable structural annotations based on experimental data in the literature. Notably, the enhanced performance of Multicoil2 is evident when tested in stringent leave-family-out cross-validation on the new database, reflecting expected performance on challenging new prediction targets that have minimal sequence similarity to known coiled-coil families. The Multicoil2 program and training database are available for download from http://multicoil2.csail.mit.edu.
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