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In this short paper, we propose the design of generic interaction scenarios that are mined from best practices (patterns).
Many studies have shown that symmetric shells appear in nature as a result of the free-energy minimization of a generic interaction between their constituent subunits.
To show this, we iteratively reassemble the helix bundle of each protein using only these interactions, generic interaction geometries, and individual helix backbone conformations.
Multiple combinations of LGR4-6, Rspo1-4 and ZNRF3/RNF43 are possible, implying the existence of generic interaction determinants, but also of specific differences in complex architecture and activity.
The class Interaction represents the generic interaction between two proteins.
A set of functions allows a generic interaction with Chado tables.
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Instead, we use a simplified model which groups multiple processes into generic interactions and use this system to guide us towards understanding what general processes need to occur within the cell and within the Wnt pathway for models to reproduce the experimental data.
Thus, although individual mutations and fitness interactions between specific sites may be different for different regions of HIV-1, the generic interactions between loci are expected to be similar and captured by the experimental fitness landscape, allowing us to employ the landscape to describe the evolution of the env region of HIV-1.
The context mining based method gave significantly lower overlap between gene sets than ISA, thus using gene sets from the context mining based method will have less chance of inferring undesirable generic interactions between similar gene sets.
Compared to the approach of context mining, conventional methods to cluster genes cannot identify gene sets that show coherent expression across a subset of samples, and thus final networks of gene sets will have only generic interactions across all samples, without any condition/subtype-specific interaction.
These observations hold for general interaction parameters and allow to infer generic patterns of the dynamics.
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