Sentence examples for rigid docking from inspiring English sources
The dockings were carried out using OpenEye's docking program FRED, [41] a rigid docking algorithm, which requires a pre-computed conformer ensemble for screening the conformational space of the ligands.
We reasoned firstly, that use of a ligand-induced protein conformation in a subsequent rigid docking protocol should deliver a similar binding mode for compounds similar to the docked ligand; and secondly that the binding mode of a ligand obtained using flexible docking should be reproduced by rigid docking into the protein conformation induced by that ligand.
Rigid docking has performed well when appropriate protein conformation is used.
In this rigid docking, the structure of the target was held fixed; the side chains were not allowed to rotate.
The applicability of high throughput screening techniques, such as blind and ligand-guided exhaustive rigid docking was assessed.
Furthermore, molecular models obtained for the four peptides in solution were used in rigid docking simulations with a heparin model.
Graphical abstract Summary of the results obtained by semi-rigid docking of crystallographic ligands.
Since only the semi-rigid docking is common to these programs, it was adopted here for the sake of comparability.
We may cite more particularly some semi-rigid docking benchmarks that include Gold, Glide, Surflex or FlexX and that were made on a large number of targets.
In order to obtain comparable results with all four programs, we used the docking method that they have in common, the semi-rigid docking, in which the target atoms are fixed and the ligands are flexible.
Benchmarks of docking programs are regularly released to compare their performance, whether by using semi-rigid docking (flexible ligand, rigid protein) [7 14], flexible docking (flexible ligand and protein) [15 17], ensemble docking (using several conformations of the protein) [15, 18] or cross-docking (docking ligands taken from some structures on proteins from other structures) [19, 20].
