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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(More)
Constraint-based models are currently the only methodology that allows the study of metabolism at the whole-genome scale. Flux balance analysis is commonly used to analyse constraint-based models. Curiously, the results of this analysis vary with the software being run, a situation that we show can be remedied by using exact rather than floating-point(More)
Reply to: A Ebrahim et al (in this issue) I n their Correspondence entitled, " Do genome-scale models need exact solvers or clearer standards? " , Ebrahim et al (2015) suggest an unnecessary dichotomy. They discuss the findings of our paper, " An exact arithmetic toolbox for a consistent and reproducible structural analysis of metabolic network models "(More)
The Multicoil-HMM algorithm offers improved prediction of coiled-coil oligomerization state. The algorithm combines the pairwise correlations of the Multicoil method with the flexibility of HMM methods. The resulting method incorporates predictors deemed important by a multinomial logistic regression to distinguish between the dimer, trimer and non-coiled(More)
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