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This section presents metrics of the ability of the predictions to correctly rank ligands by affinity. The rankings were evaluated in terms of the Kendall's τ, Spearman's ρ, and estimated binding energies for the free energy sets were additionally evaluated in terms of centered root-mean-square error (RMSEc, kcal/mol) and Pearson's r. Uncertainties in these statistics (e.g., Kendall's τ Errors in the table) were obtained by recomputing them in 10,000 rounds of resampling with replacement, where, in each sample, the experimental IC50 or Kd data were randomly modified based on the experimental uncertainties. Experimental uncertainties are added to the free energy, ΔG, as a random offset δG drawn from a Gaussian distribution of mean zero and standard deviation RTln(Ierr). In this evaluation, the value of Ierr was set to 2.5.
For the kinases, a number of experimental Kd values were reported as ≥10 µM, making them difficult to include in standard metrics of ranking accuracy, so these cases were excluded from these affinity ranking assessments. However, they are included in the Active/Inactive Classification assessments, below.
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