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Positive binding affinity was defined as an absorbance for immobilized nmAb-KT that was 2-fold above the background or negative controls.
The impact of a SNP on TF binding affinity was defined by comparing the observed score difference to the distribution of PWM score differences from 10,000 matched randomly selected SNPs from the Illumina 660K SNP array (see Methods).
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For instance, if the i-th base of the reference motif and a specific binding site is m i and f i, respectively, the retained binding affinity is defined as μ i, m i, f i ; 3) a vector that denotes the optimal base pairing probability of k bases in the motif θ = (θ i); and 4) the penalty for the deviation from the optimal base pairing probability α.
The apparent binding affinity was derived from 3 or more experiments.
The distance cutoff in the scoring function defining which pairwise interactions are taken into account when estimating the binding affinity was estimated based on a benchmark set of MHC class I binding data described in the methods section.
HER2 binding affinity was determined in saturation radioligand binding assays using SKBR-3 cells (1.3 × 106 HER2/cell).
(B ) The binding affinity was calculated at −8.9 kcal mol−1.
The binding affinity was calculated at −8.9 kcal mol−1.
This indicates that even though the binding location of DB00631 fluctuates with different peptides, the overall binding affinity is conserved.
Notably, their effect on binding affinity is much less pronounced.
Interestingly, we found that target-binding affinity was modulated by residues in the guide region.
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