In the construction of a protein-protein interaction table, information on interaction types, directions of interactions, and cell lines is collected in addition to the identities of interacting proteins.
Information theoretic approaches do not predict the directions of interactions which are important in understanding the signal flow via biological pathways [ 11].
In the present application, as introduced in Schneidman et al. (2006), it is related to the likelihood that a spike occurring in 1 neuron will "cause" a spike in another neuron or vice versa (the directions of interactions are not estimated by this model).
A strict analysis shows that a specific coupling of multi-atom Van der Waals interactions with covalent bonding can, in extreme cases, increase (or decrease) the interaction energy by about 20 40% at certain angles between the direction of interaction and the covalent bond.
The correlation measure of the entire data is beneficial for determining the strength of association between nodes (see Section 2.4) but disadvantageous for detecting the direction of interaction.
Modification of the main structural fragment of a drug may lead to an improvement in its antimicrobial efficiency and strength as well as mode and direction of interaction.
'Direction of interaction' indicates that one protein affects the activity of another protein, i.e. upstream or downstream in the signaling pathway.
Interestingly, AGRIS did not list the direction of interaction between AGL15 and four of the genes regulated by it (AGL22, AGL25, EDF4 and RAV2).
