Clustering Molecular Dynamics Trajectories for Optimizing Docking Experiments

Figure 3

Clustering validity criteria for the MD trajectory of the InhA enzyme as a function of the number of clusters. (a) Gap statistic. (b) Dunn’s index. (c) DB index. Black circles identify the best number of clusters for each criterion. The best gap result was used as the decisive criterion for selecting between and , as suggested by Dunn’s index and DB, respectively.

(a)

(b)

(c)