Knowledge networks consisting of links between knowledge elements and social networks composed of interactions between inventors both play a critical role for innovation.
The interface is composed of interactions between N- and C-terminal α-helixes and of loops between α-helixes and β-sheets of both monomers [59].
Details of the derivation of reaction rates of the time-continuous model are given in the Additional file 2. According to the network wiring validated in the logical model checking step (see " Results"), the final continuous model was composed of interactions given either by the production or degradation reactions of c-di-GMP.
The domain structure is composed of interaction domains a few hundred nanometers in size, which indicates the presence of a strong exchange coupling between the grains.
Because interaction data is known to be noisy, we also generated a filtered PIN composed of interaction supported by more than one independent experimental methods.
For example, given that A and B have been validated experimentally, if protein A is homologous to C and D, then protein B is homologous to E and F. Consequently, the final mapping result will be composed of interaction pairs of CE, CF, DE and DF (Fig. 1A).
Second, we combine 37,177 interactions whose confidence scores are at least 90% in the InterDom database and all interactions in the DOMINE databases to obtain a large domain-domain interaction network that is composed of 48,778 interactions between 5,490 domains (17.77 interactions per domain on average).
For this purpose, we implement the same validation process based on the large compiled domain-domain interaction network that is composed of all interactions in the DOMINE database and high-confidence interactions in the InterDom database.
First, we discard singletons in the PDB part of the DOMINE database [ 23] and obtain a small network that is composed of 2,285 interactions between 1,971 domains (2.32 interactions per domain on average).
In order to validate this assumption, we discard singletons in the PDB part of the DOMINE database [ 23] and obtain a domain-domain interaction network that is composed of 2,285 interactions between 1,971 domains.
We perform this ab initio inference using the large network that is composed of entire interactions in DOMINE and high-confidence interactions in InterDom (with diffusion kernel), and we summarize the results in Table 6.
