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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).
It is proposed to develop communal system to serve residents in densely populated cluster with proper tariff system.
This likely took place when both stars were only a few tens of millions of years old and still resided in a densely populated cluster, the pair reports in the 2 December issue of Nature.
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.
A cluster analysis was performed and the ligand conformation with the lowest binding energy lay also in the more populated cluster.
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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Phylogenetic analysis shows the presence of many clusters of Clp protease-like proteins and significantly populated clusters were identified for Firmicutes, Gammaproteobacteria, Cyanobacteria and Actinobacteria.
In Level 2 of the hierarchy, the energy separation between the conformational sub-states become even more apparent: 73% of the conformers populate cluster I; others populate two low energy (clusters II and III) and one high energy (cluster IV).
If only the Portal is used, many phages populating Cluster 4 are spread in different branches of the tree irrespective of the nature of their hosts (highlighted by a mark in Additional file 1: Figure S5A).
Depending on the distance criterion used for populating the clusters, hierarchical clustering is divided into the following major categories and their alterations: single-linkage clustering, complete-linkage clustering and average-linkage clustering; in Table 2 some of the most common agglomeration methods are described.
We moved through its narrow corridors and paths, which were populated with clusters of umbrella-toting Chinese and sunburned Russian tourists who eyed the spaces around them absently with stares that groped about for miles.
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