This offers high-quality docking that depends on a novel optimization technique.
As such, the level of convergence for some ligand atoms is quite high, because even low-quality docking solutions leave the positions unchanged for those atoms.
Docking protocol was evaluated through re-docking process in which the co-crystallized compound was extracted and re-docked into the binding cavity, and the quality of docking protocol was evaluated through root mean square deviation (RMSD ≤2 Å is considered as best).
The conformation of an activated GPCR results in limited ligand accessible volume, significantly reducing the quality of docking results.
It should be noticed that despite good positioning quality the docking program is not always able to distinguish good inhibitors from excellent ones and bad inhibitors from inactive compounds and consequently the false-positive and false-negative results appear in the virtual screening process.
Moreover, the quality of the docking process was attributed to the good overlapping of compound 24 with ribavirin in the active site (Fig. 4).
The quality of the docking score depends on two factors: the scoring function and the search method being used to find the lowest binding energy solution.
The docking quality is typically measured by a scoring function: a mathematical predictive model that produces a score representing the binding free energy and hence the stability of the resulting complex molecule.
We realized that the correlation in this set of protein-compound pairs should not be used to judge the quality of the docking programs.
The screening quality of the docking methods using energy-based scoring functions alone is often influenced by the structure of the ligand screened (e.g., the numbers of charged and polar atoms).
This docking quality is considered usually as "good" one.
