Illustration of the difference between the Elastic Networks.

(A) Superposition of the initial structure (gray) of the atomistic MD simulation and the average structure (blue). (B) ELNEDYN network based on the crystal structure/initial structure of capsomer protein A from the PDB entry 1ZA7. (C) First step of the IDEN elastic network definition using just the distance criterion. When the distance criteria alone is used for elastic network definition it gives rise to artifacts such as the constraining of the flexible N-terminal tail (region pointed to by arrow) (D) The bonds that are removed from the network definition from (C) according to flexibility and concerned motion using the IDEN definition. (E) Final IDEN elastic network. The cyan arrow points to the unconnected N-terminal tail and the red arrow points to a loosely connected loop region by comparison to the network shown in (C).