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The calculated binding free energies in terms of MM-PBSA method are consistent with experimental ranking of inhibitor effectiveness for the four inhibitors.
10 The wpc-index is normalized to a final value that ranges from (0,1); the higher the normalized wpc-index, the more similar the predicted ranking is to the experimental ranking.
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The experimental ranked list was based on the difference between the experimentally determined IC20 (20% inhibition concentration) and the expected IC20 (20% inhibition concentration) for pairs of drug combinations.
The weighted Euclidean distance measure was compared to other similarity/statistical measures in subchallenge 2. Each method had a score (wpc-index), which was calculated by comparing the predicted ranked list of the 91 drug pairs to the experimental ranked list (the ground truth).
If the predicted rankings between the two cell lines correspond to their experimental rankings, then a value between (0.5,1) is returned according to an error function (e.g., the error function takes into account the ranking (predicted vs. experimental) as well as the response (predicted vs. experimental) of the cancer cell lines to drugs).
In addition, the experimental cycle rank order closely matches with that determined by modeling.
In E. coli UlaG, experimental evidence ranks Mn2+ and Co2+ as potential binders, since they display similar binding profile and both facilitate catalysis on L-ascorbate 6-phosphate, and singles out Zn2+ as a potential competitive inhibitor of catalytic activity.
It has three parts: (i) the drug interaction scoring and prediction in the core genes set (left side of Figure 2); (ii) the drug interaction calculation from the observed dose response curve (right side of Figure 2); (iii) the probabilistic concordance (PC) index calculation between the experimental drug interaction ranking and the predicted drug interaction ranking (the bottom of Figure 2).
It was found that the pressure transient was reasonably independent of the dynamic impedance of the plate, suggesting that the metal foam projectile is a convenient experimental tool for ranking the shock resistance of competing structures.
Random corrected 4C-seq and ChIP-seq samples were correlated by ranking experimental values within restriction fragments (Table 1).
The RST system ranks experimental MS/MS peaks by increasing order of intensity, computes the intensity rank sum of peak matches, and estimates the P value of obtaining a better rank sum by random chance via a normal distribution [18].
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