Fig. 2.

Structural deviations along ADK transition pathways. (A) Deviations (rmsd) between the succession of two intermediate states generated from open and closed ADK, respectively, as analyzed with the simple harmonic potential (blue), with the bond-restrained potential (red), and with the VAMM potential (green). (B) Deviations during the VAMM-based transition calculations. An expanded view is shown for deviations (rmsd) between the succession of VAMM intermediate states as they move, frame by frame, from the respective closed (Left) and open (Right) states toward similar terminal intermediates (blue). Deviations between the closed state and intermediates generated from the closed state (green) and deviations between the open state and intermediates generated from the open state (red) are also shown.