Implications from a Network-Based Topological Analysis of Ubiquitin Unfolding Simulations
Figure 5
Identification of Transition State: Projection of the RMSD between all pairs of frames onto a 3D cartesian coordinate.
The frames were 50 ps apart. The line connecting two two conformations implies sequential evolution in time. The distance between the conformations is proportional to the RMSD distances between the conformations.