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When a particular protein was assigned to more than one functional classes in MIPS database, we computed the coefficient of functionality for each functional class to which the protein belonged and then designated the protein to be belonging to that particular functional class which showed the largest value of the coefficient of functionality.
As for an example, if the ith protein in the PPI networks have m PPI partners and in which n partners belong to the same functional class then we computed the coefficient of functionality of the ith protein as n/m.
Thus the coefficient of functionality is related to the protein connectivity in the overall PPI network.
The Pajek software calculates the clustering coefficient of the proteins in the PPIs network independent of their classification based on the coefficient of functionality.
A recent study revealed the importance of the features of the interacting protein partners, viz., the coefficient of functionality and clustering coefficient in controlling the protein evolutionary rates in a protein-protein interaction (PPI) network.
This is the interrelationship between the features, viz., the expression level, complex forming ability and the coefficient of functionality, that guided the difference in evolutionary rates of DF and SF proteins.
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When the cut-off for coefficient of functionality and clustering coefficient were changed over a wide range of values, our results still remain unchanged while detecting influences of various factors in protein evolutionary rate in this study.
Recently it was suggested that protein evolutionary rate is related to the features of interacting partners in a protein-protein interaction network [ 18], viz., same or different functional (SF or DF) proteins - based on coefficient of functionality and sparse or dense part (SP or DP) proteins - based on the clustering coefficient [ 18].
This correlation suggests that coefficient of functionality decreases with increasing connectivity, i.e., the DF proteins should have higher connections than SF proteins.
In our study, we have analyzed the evolutionary distances in yeast proteins by taking into account the various evolutionary forces and including the features of interacting partners in a protein-protein interaction network based on coefficient of functionality and coefficient of clustering.
It's the vulnerability to loss that is the coefficient of the depth of feeling.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com