Figure 2.

Schematic explanation for simulations of conformational change. First, the set of displacements {Δq_i}_i=1,2,…,3N for all Cα atoms in the (n–1)-th structure are calculated (N is the number of Cα atoms). {ΔQ_i}_i=1,2,…,N are three dimensional vectors whose x, y and z components are Δq_3i-2, Δq_3i-1 and Δq_3i. As candidates for the n-th structure, two structures are built, by deforming the (n–1)-th structure to positive and negative directions of {Δq_i}. Then one of them with the smaller heavy-atom RMSD against the open state is selected. If the structural consistency is preserved, this structure is chosen as the n-th structure.