The poses were ranked on the basis of this overlap measure, and the pose with the best overlap was selected as the most likely binding mode (Kozakov et al. 2011) (for a detailed description of this analysis, see Supplemental Material, "Computational analysis of ligand binding to PPARγ").
In hMADS, AHR expression was similar at the two cell stages and was significantly decreased by the treatment with AhR ligand in precursors (see Supplemental Material, Table 1).
Amino acid sequences alignments of the identified tetrapod and teleost Egf receptors and of the mature Egfr ligands are shown in [Additional file 1: Supplemental figure S1B] and [Additional file 2].
The docking program successfully reproduced the original binding pose of the native ligand with an excellent docking score (−13.5, Supplemental Fig. S4).
The size of the pocket allows for binding of various ligands at this position in various orientations (see Supplemental Material, Figure S5).
To further evaluate these differences, the binding affinites for several of these ligands were calculated by SPR (Table 1 and Supplemental Fig. 3).
According to the macro-synteny analysis, Dre5, Dre8 and Dre21, Tni12 and Tni4, as well as Ola9 and Ola12 share numerous orthologous genes with the ligand cluster region on Hsa4 [Additional file 4: Supplemental figure S7].
Therefore, supplemental treatment of mothers or direct treatment of newborn infants with natural ligands for PPAR would be an alternative method to increase UGT1A1 expression to accelerate bilirubin conjugation in infants.
Western blot analysis (supplemental Figure S2) showed that the allosteric antibody WC75 and the ligand competitive antibody WC613 both immunoprecipitated Notch1 but not Notch4.
[Additional file 7: Supplemental figure S9B and S9C] display the interface between receptor and ligand in more detail.
The overall view [Additional file 7: Supplemental figure S9A] outlines the three main interaction sites between receptor and ligand.
