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In each Shaker cycle, distance and energy metrics are calculated describing target-ligand interactions at each time step (frame) of a trajectory.
Representative data from one A431 and one U343 affinity measurement is depicted in figure 2. Residuals plot were calculated, describing the differences between the measured data and the calculated fits.
We have assessed the predictive ability of the method using an elaborate stratified double cross‐validation procedure, involving the fitting of a sigmoid function on the raw output from SVM. Precision and recall values for each GO‐BP function were calculated, describing in detail the performance of the prediction.
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CPIS was calculated as described in a previous report [ 2].
Parameters were calculated as described previously [5],[6].
Significant differences were calculated as described before.
They are calculated as described next.
CoV was calculated as described previously [20].
The PAM score was calculated as described previously.
The PER values are calculated as described in the Appendix.
Means and confidence intervals were calculated to describe the outcomes.
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