… the LIE method are combined to predict binding modes and estimate binding free energies
for … The GOLD docking program (4, 5) is used to predict the binding modes for the inhibitors. …

… most of them similar binding modes are observed for … binding mode observed during the
production phase of the MD simulations. Amber95 reproduces the experimental binding mode …

… followed by an energy minimization step at the active site, we will most likely get very close
to the true binding mode. … energies appears quite evident since we intend to apply the linear …

… In addition, the results from the scoring functions are compared to a more rigorous
technique, the linear interaction energy method (LIE). (9) The scoring functions and the LIE …

… used in the linear interaction energy method. The proposed … possibility that multiple binding
modes contribute similarly to … The method was applied to a set of 12 compounds binding to …

… In addition, to investigate the favored binding mode, ligands were manually docked in the
crystal structure of the ERα LBD in all possible orientations, as illustrated for E2 in Figure 1. To …

… binding free energy method, its effective potential energy … binding modes sampled by the
BEDAM with flattening at λ b = 1 were stabilized by non-native ligand intramolecular interactions…

… structure available and the ligands of each protein system share common scaffold, (27−34)
for each protein–ligand complex, a top docking pose which is also close to the binding mode …

… and unfavorable binding modes which are coupled through the normalization of the … potential
energy function describing direct covalent and noncovalent intramolecular interactions as …

… scoring to predict the ligand binding free energy. Compared to free energy methods [25], it
… met and the obtained value of the mean MMPBSA interaction energy (Table 12). Thus, we …