Sentence examples for by the docking program from inspiring English sources

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.

All the poses output by the docking program are saved to a file, while their scores and rankings are ignored.

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.

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.

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.

The fitness landscape of the docking program is modeled by a modified version of the scoring function X-Score [1].

We previously verified[ 24] the suitability of the crystal structure for use in docking studies by removing the cocrystallised androstenedione from the substrate binding site and using the docking program GOLD[ 51] to dock the steroid back in.

Both docking scores were within the standard error of the docking program suggesting similar binding affinities.