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Lennard-Jones (LJ) parameters for ion-ion and ion-water interactions are from the literature, and are used along with Lorentz-Berthelot mixing rules [28].
In this analysis all bacteria sequence information is downloaded from [ 24] and all preliminary gene/TF interactions are from [ 14].
The dataset is from Spellman's experiment [ 19], and the interactions are from Saccharomyces Genome Database (SGD) database.
It currently contains 204,705 unique DDIs between 7,351 distinct Pfam domains, where 6,768 interactions are from 3D structure-derived datasets.
> -wrap-foot> > -wrap-foot> The breakdown by organism shows that the majority (59%) of the consolidated physical interactions are from the yeast Saccharomyces cerevisiae (30%) and human (29%); 13% are from fly (Drosophila melanogaster) and 7% are from various strains of Escherichia coli; whereas those from the worm C aenorhabditis elegans, mouse and rat each represent <4%.
Many documented interactions are from limited and small case reports and clinical observations and the details around the interactions are sparse, however they support that some herbal medications or supplements have potentially harmful side effects as well as adverse interactions with conventional drugs.
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The transcription factor interactions were from the yeastract database (literature curated once) [ 27].
Depending on the details of evolutionary dynamics, time since introduction could influence how different the 'familiar' interaction is from the corresponding 'unfamiliar' interaction.
These interactions are interesting from a policy perspective.
First, the protein-protein interactions are collected from PIBASE, a database of protein interaction structures [21].
In total 1,383 non-redundant binary protein interactions are extracted from the high-resolution structures.
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CEO of Professional Science Editing for Scientists @ prosciediting.com