RMSD-based clustering

In Durrant et al. (47), RMSD-based clustering was performed using an RMSD cutoff of 0.085 A on a subset of residues that line the ATP binding site, which are residues 87-90, 155-162, 207-209, 283-287, and 305-308. 

Table 15.1 Scoring results (GOLDSCORE) for periodical extracted structures versus ensemble representation by cluster representatives generated by RMSD-based clustering on the active site atoms shown in Fig. 15.1a-c. In the weighted average score, the scoring values for cluster representative structures are multiplied with the population of the respective cluster in the MD simulation...

Figure 5.13 (A) The lowest COST poses for the NOE matching run on Bcl-xL/7 were clustered based on RMSD to each other. The individual poses for each of the 10 lowest COST clusters were ordered based on COST and plotted from lowest COST to highest COST Members of the different clusters are indicated with distinct symbols. All of the lowest COST poses belonged to one of two clusters, as shown in (B). (B) COST versus the RMSD (A) to the cluster 2 centroid for Bcl-xL/7. Member poses of the 10 lowest scoring clusters are indicated as in (A).

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