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Finally, the average of the AbrB-binding signals within the individual binding sequence was calculated, as the AbrB-binding signal intensities of each binding site.
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Immunoprecipitated DNA was analyzed for p53 occupancy on selected chromosomal sites surrounding the predicted miR-associated p53 REs by RealTime-qPCR and fold enrichment of p53 binding to the respective DNA sequences was calculated by the comparative Ct method as described previously [ 47].
A neighbor-joining tree of these sequences was calculated with SEMPHY74.
The binding scores for these random sequences are calculated, and the number of scores that falls into each bin is denoted by n b.
The binding constant was calculated to be 4.57 × 104 M−104
Binding energy was calculated by applying CHARMm forcefield.
Binding energy was calculated using the mapping with offset from −4 to 4. To evaluate DREAM4 gold standard, 104 sequences were generated using the gold standard PSFM.
An average binding ratio was calculated ± one standard deviation.
The binding affinity was calculated at −8.9 kcal mol−1.
The number of ADP binding sites was calculated.
(B ) The binding affinity was calculated at −8.9 kcal mol−1.
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