Figure 5. Ligand binding pocket flexibility within comparative models compared to experimental structures.

For each of the 26 pocket residues in the ligand binding pocket of the receptor, pocket collapse is defined as the change in distance from each pocket residue to the ligand, measured between the model and the experimental structure. A positive pocket collapse value indicates that the pocket residue moves closer to the ligand in the model compared to the experimental structure, while a negative pocket collapse value indicates movement towards the receptor. The width of the beanplot area represents the number of models having a pocket collapse of a certain value for the threaded models (blue) and for all generated comparative models after loop rebuilding and energy minimization (orange), with corresponding blue and orange horizontal lines representing the average pocket collapse over the given set of models.