Fig. 6.

Overview of a bootstrap method for structure comparisons. An ensemble of possible conformations is generated for each of $m\in M$ proteins using MD simulation. For each of $n\in N$ trials, a conformation c_m is randomly selected from each of the M ensembles to populate a new trial data set C_n. Pairwise comparison of the conformations in each trial data set C_n generates new distances from which a NJ tree T_n is created. Each trial tree, T_n, is compared with the reference tree T₀. If a relationship between structures in the reference tree T₀ is recreated in the trial tree T_n, it is counted. The nodes of T₀ are labeled with the fraction of trial trees in which the relationship was recovered, providing a measure of the statistical support for that node.