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b Comparison of interactions between glycine and TiO2, mica, or pyrite by TDS measurements.
In order to facilitate the comparison of interactions across species, we first surveyed the amount of gene conservation between species.
As exemplified by this use case, eFIP enables the investigation of phosphorylation-dependent PPIs in a particular biological context (e.g., disease) and comparison of interactions across different contexts.
Structural comparison of interactions between EF3-4, Zr-7, and the neck reveals the basis for the higher affinity of α-actinin-2 for titin versus the pseudoligand neck (Young and Gautel, 2000).
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We present a detailed comparison of interaction modes with the natural product inhibitors tunicamycin and muraymycin D2.
The comparison of interaction energy diagrams (Additional file 1: Fig. S7; see also Tables S1 S6) shows that this packing similarity results in a striking similarity of corresponding pairwise interaction energies.
The potential role of intermolecular hydrogen H⋯F bonds stabilizing the crystal structure was estimated by mutual comparison of interaction energies for parallel-stacked and parallel-displaced dimer configurations.
Although this assay cannot be used to measure kinetic parameters, a comparison of interaction intensities detected on peptide arrays with published dissociation constants between several effectors and various histone ligands, a general pattern emerges suggesting that interactions that are ≤150 300 uM Kd range can be detected on the arrays (Fig. 3; Table S3; data not shown).
Box plot for the comparison of interaction frequencies between real data and random background.
The additional interactions are included only to allow for a comparison of interaction sets of equal size.
Our approach is based on comparison of interaction networks from various species and utilizes orthology relationships, conserved modules and local PPI neighborhoods.
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