Figure 1. Reconstruction of the structural landscape by PCA from structurally rich ensembles and generation of transition pathways by eBDIMS.

The workflow is shown for a typical example (RBP, details in Fig. 2): structures are collected from the PDB (left panel) and the end-states are selected based on the literature; the ensemble is aligned to the inactive or apo state of the protein for PCA, and forward and reverse trajectories are independently computed with the eBDIMS sampling method (middle panel). Finally, the two principal PCs are used for projection analysis of the trajectories (right panel), allowing for straightforward detection of on-pathway intermediate states.