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In examining chemical reactions, it is useful to consider several general subjects: (1) factors that influence the course of chemical reactions, (2) energy changes involved in the course of a typical reaction, (3) factors that reveal the mechanism of a reaction, and (4) the classification of reaction mechanisms.
As in some earlier work, the principal results rely on a classification of reaction networks by means of an easily computed non-negative integer index called the deficiency.
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The classification of reactions into pathways was retrieved from the KEGG database.
The following step aimed to investigate in detail the classification of reactions into the actual pathways.
Moreover, the classification of reactions into phylogenetic reaction sets is generally in agreement with classifications obtained using different procedures [ 15].
To address this question, I took advantage of the biochemical pathway classification of reactions in KEGG [ 36].
The classification of reactions into pathways is somewhat subjective, since it can be implemented in a varied manner.
Classification of reactions by functional category as presented in supplementary figure S1 (Supplementary Material online) follows previous authors (Reed et al. 2003; Duarte et al. 2004).
Second, the characterization of the set of reactions in species, as well as the classification of reactions into phylogenetic groups is dependent both on the sensitivity of the homology assignment procedure and the range of species analyzed.
This classification of reactions is especially important in constraint-based modeling that covers whole-cell metabolic networks and depends on the knowledge of reaction directionality for predicting flux distributions, growth rates and other large-scale metabolic phenotypes (Beg et al., 2007; Burgard et al., 2003; Oberhardt et al., 2009).
Thus, it is necessary to replace the rigid priori classification of reactions into reversible and irreversible ones by a more flexible constraint that assures the flux directions to be compatible with the change of Gibb's free energies, exhibiting a wide range of values depending on the actual metabolite concentrations.
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