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While all the RMSD and ST ST-opt average accuracy measures did linearly correlate with the RMSD cluster value (Figures 8 and 9).
Cluster and exponential error is calculated as the percentage difference between measured thickness and either the average cluster value, or the value predicted by exponential regression.
As the RMSD cluster value (as well as N NHA, N R and N ER ) increases, all five conformer model accuracies before and after clustering linearly changed.
If the conformer model had more than 500 conformers after sampling, it was re-clustered with the RMSD cluster value incremented by a further 0.2.
Approximately 85% of the 47,123 PDB ligands have an RMSD cluster value of ≤ 1.0 Å. Figure 3 RMSD cluster conformer model sampling threshold.
Looking at the 90% level of conformer models before and after clustering, there are some variances in the change of the conformer model accuracy, depending on the RMSD cluster value.
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The frequency of the RMSD clustering threshold (RMSD cluster ) values used during the conformer clustering procedure for the 47,123 MMDB ligand conformer models.
The second step considered recalculating new cluster values.
The cluster values for this parameter were Cluster 1, 0.530; Cluster 2, 0.547; Cluster 3, 0.557; Cluster 4, 0.563.
Logarithm transformations were applied to the metabolomics cluster values to improve normality.
For each comparison, at least 10 000 permutations were computed to build a distribution of cluster values.
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