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A good correlation was found between the binding score of the monomers and the affinities of the corresponding polymers.
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Our observations are further supported by Pearson's correlations between the binding scores of different Hox proteins (Fig. 1c).
Besides miRNA and its target mRNA, other information, such as the sequence of miRNA/mRNA, the binding score between miRNA and mRNA and number of conserved and non-conserved sites, may be also presented in each row depending on the miRNA-target prediction algorithms used.
The refined candidates were ranked by the binding score.
There is the same trend between the downregulation experiments and the binding scores.
Only the sequences with at least 80% of the maximum possible binding score on either of the alleles were further studied by computing the absolute difference of the binding scores between the alleles.
For a better comparison between the binding free energies of the PCBs and BphA, the binding scores were converted to binding free energies (kcal/mol).
Comparison of the binding scores of these consensus binding clusters between the two replicates revealed a high correlation (R = 0.619) (Supporting Information Fig S1E).
Then, target proteins are ranked according to the binding scores estimated by a scoring function.
The correlations between the predicted binding scores of individual scoring function and the experimentally measured binding affinities range from 0.644 to 0.216.
In the training, we attempted to obtain highest Pearson's correlation coefficients between the predicted binding scores and the measured Ki or Kd values.
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