Figure 4
From: Predicting protein ligand binding motions with the conformation explorer
Predicted conformational change. The apo, or starting structure used as a starting point for the calculation is shown in orange on the top row. The M domain of this molecule is rotated with respect to the S domain until converging to the predicted structure (blue trace, bottom row). These generally align well with the known holo structures (green cartoons, superimposed on the blue, bottom row). Molecules are displayed such that the S domain is in the right-hand portion of each molecule, the M domain is in the left-hand portion, and the hinge is between them, with the binding cleft opening downwards. The predicted and holo structures are aligned based on the S domain (as for the sRMSD calculation) to highlight the degree of alignment of the M domains.