Sentence examples for by the docking programs from inspiring English sources
The molecules chelating exotic atoms (Au, Cu, Hg, I, Sn, …) or ions (Fe2+, Mg2+, …) were also filtered because they were not correctly handled by the docking programs.
Two of these proteins, aofb and casp3, are covalently bound to their crystal ligand, so they were excluded from the dataset because they cannot be properly handled by the docking programs in their standard usage.
We have shown here that, compared to simply ranking the poses output by the docking program according to a single docking score, an initial filtering of the docked poses with a pharmacophore query to remove poses that do not form certain essential interactions with the target binding site greatly improves the quality of the results.
However, implementing molecular docking, for studying the interactions between a pair of proteins poses a challenge to identify the best-docked pose out of the pool of various poses suggested by the docking program GRAMM.
Interactions of ligands with metal ions can be recognized by the docking program only for certain ligand protomers or tautomers [38].
We have developed a simple method for reducing the number of false positives in a virtual screen, meaning ligands which are scored highly by the docking program but do not bind well in reality.
Although we have not compared our method directly with these constrained docking methods, we would anticipate that the enrichments seen would be quite similar (if not better with constrained docking because the conformational search done by the docking program is biased in favor of solutions that fit the constraints).
Unlike a traditional pharmacophore search, the ligands do not need to have low-energy conformers generated, or be translated or rotated to align to the pharmacophore hypothesis because they have already been aligned to one another in the coordinate space of the binding site by the docking program.
Note that its FEB value of -8.27 kcal/mol is greater than the best one (-8.99 kcal/mol) ranked automatically by the docking program.
The fitness landscape of the docking program is modeled by a modified version of the scoring function X-Score [1].
