Characterization of Promiscuous Binding of Phosphor Ligands to Breast-Cancer-Gene 1 (BRCA1) C-Terminal (BRCT): Molecular Dynamics, Free Energy, Entropy and Inhibitor Design
Fig 3
Ligand L1 is shown in green licorice structure. Only residues within 7 Å of the ligand (live set, labeled in blue) is set flexible in M2 calculations. The rigid set (real set, labeled in yellow) contains the residues within 5 Å of the flexible set; other atoms outside the real set (labeled in pink) were not considered during M2 calculations. Notably, the computed entropy and enthalpy terms from M2 consider the contribution of BRCT (live set) and the ligand.