Figure 6

Effect of altering the geometry or chemistry of the binding groove on PM ₁₃ Scores. Altered binding grooves are compared with the original using PocketMatch₁₃. PM₁₃Scores calculated with different distance element alignment thresholds are shown in different colours (1.0 Å in purple; 0.75 Å in cyan; 0.5 Å in red; 0.25 Å in green; 0.125 Å in blue). (A) The coordinates of atoms in the binding groove of [PDB:1JWS] (A, B, C chains) were perturbed randomly, and an ensemble of 1000 structures was generated with RMSD values up to 5 Å with respect to the original [PDB:1JWS] structure. (B) The atomic group labels of some of the atomic groups in the binding groove of [PDB:1JWS] (A, B, C chains) were re-assigned randomly.