Figure 3.

Pocket detection limits. Left: Example of PDB entry 1esa. A large part of the ligand is outside the pocket detected by fpocket. Despite this fact, a criterion such as the PocketPicker criterion would accept the pocket as successfully identified, and the Mutual Overlap criterion not. Right: Example of PDB entry 1w1p. The identified pocket is large compared to the ligand. Its centre of mass is too far from any atom of the ligand for the Pocket Picker criterion to accept it as successfully identified. Ligands are represented using a ball and sticks representation. Alpha sphere centres are represented as small spheres, and their envelope is depicted in brown.