Ligand conformation ensembles

Figure 5 The frequency of protein conformations for the SB203386-HIV-1 protease complex in docking simulations with the ensemble of 6 protein conformations (a) and the ensemble of 32 protein conformations (b). The piecewise energy function is used. The unfilled histogram is the total frequency for each conformation, the filled histogram is the frequency for ligand conformations that are within 2.0 A RMSD of the crystal structure.

Because the receptor conformations are changed concurrently with the ligand conformations, a 4D simulation convergence time is comparable with that of a single receptor docking, and is significantly shorter than for the traditional ensemble docking ... 

The programs described above were used to generate ensembles of conformations for each ligand in the test set. Finally, all conformations were compared to their corresponding bioactive geometry. A hit was defined when at least one conformation was found within an ensemble with an RMS fz deviation to the x-ray geometry less than or equal to 0.5 A. 

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