Fig 1. Analysis of HER2/pertuzumab complex.
(A) Structure of the HER2 (green)/pertuzumab (yellow) complex. The fragment from Glu46 to Lys65 of pertuzumab is shown in red. The side chains that participate in key interactions are shown as sticks. Calculated distances (< 5 Å) are indicated with blue dash lines. (B) Backbone RMSDs as a function of time for the initial and successive structure of HER2/4665 complex in MD trajectories. (C) Binding free energies and individual energy terms for HER2/4665 and binding free energy decomposition for each residue of 4665. (* means that ΔGtot does not contain -TΔS energy)