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The most populated clusters, accounting for 31, 65, and 26% of the overall population, had the first occurrence at 41, 11, and 39 ns, and no new clusters with a population ≥5% appeared after 46, 11, and 51 ns for NtrC, CheY, and FixJ, respectively.
Considering the most populated clusters (and not the lowest energy), 42 first rank and 9 second rank results were observed.
The representative conformations of F4HBoNTAe and F3ABoNTAe from their most populated clusters overlay reasonably well (see Figure 3) and are considered as plausible complex structures in water.
Of the three most populated clusters (Figure 4), the AHP conformations in Clusters 1 and 3 are similar, and the one in Cluster 2 is unique.
As expected from PCA, the two most populated clusters were number 4 and 8, composed by genes modulated positively and negatively from TP B to TP C, respectively.
The data used to generate Table 1 was taken by looking at the most populated clusters for each elongation factor in the NCBI Protein Clusters Database [ 34].
Similar(53)
An all-heavy-atom RMSD threshold was chosen to give 1/6 of the clustered models in the most populated cluster, as in prior work (Das et al., 2008).
Considering the most populated cluster (and not the lowest energy) as a first rank result, 30 of the 53 dockings were able to successfully predict the experimentally observed binding mode.
In all cases, where the most populated cluster's frequency was above 50 out of 100 runs, the result was accurate (with an RMSD below 2.0 Å as compared to the X-ray structure).
All 1800 conformers from the most populated cluster (Cluster 3) of the first-round cluster analysis were subsequently subjected to a second-round cluster analysis using the averagelinkage algorithm (epsilon = 1.5 Å and RMS on all atoms of residues 74 78).
For this purpose, we performed a clustering analysis on each of the MD trajectories to identify the most populated cluster from which a representative structure could be derived to compare with the starting structure.
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most successful clusters
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most populated places
most genetic clusters
most prevalent clusters
most populated chemotypes
most similar clusters
most globular clusters
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most common clusters
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most pr19RNA clusters
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