Multiple unbinding pathways.
The red/green coloring illustrates the distance between centers of mass of BUT and FKBP active site. To illustrate the unbinding pathways, all frames of the 50 MD runs are first overlapped in space  using the coordinates of the C atoms of FKBP. The different positions and orientations of BUT are then clustered according to DRMS with a threshold of 1 Å. (Top) Stereoview of the most populated clusters. The radius of the spheres is proportional to the natural logarithm of the corresponding cluster population. (Bottom) Ligand unbinding network colored according to the distance between BUT and FKBP. Nodes and links are the clustered conformations and direct transitions, respectively . The size of each node is proportional to the natural logarithm of its statistical weight. Only the 4184 nodes with distance between the centers of mass of the ligand and FKBP active site smaller than 15 Å were taken into account; of these, only the 2918 nodes with at least two MD snapshots are shown to avoid overcrowding. Nodes of the bound state, i.e., those in Fig. 2, bottom, are all included in the dense region of red nodes on the left.