Sentence examples for binding mode of ligands from inspiring English sources
Docking programs are used primarily to predict the binding mode of ligands to receptors.
We report how computational modelling predicted the binding mode of ligands of special interest to the Chk1 ATP site, for representatives of an indazole series and debromohymenialdisine.
Water can form complex bridging networks and can play a critical role in dictating the binding mode of ligands.
Recently, the combination of NMR data such as ligand-induced chemical shifts and docking calculations was proposed to rapidly and efficiently obtain information about the binding site and binding mode of ligands [13] [15].
The benefit of docking is to identify the binding mode of ligands in the binding pocket of protein through specific key interactions and to predict the binding affinity between the protein-ligand complexes [ 32].
In several independent studies, the Y537S surface mutation has been shown to stabilize the active conformation of the receptor, and, in turn, facilitate crystallization of weak agonists without modifying either the overall architecture of the LBD or the binding mode of ligands (Bruning et al. 2010; Delfosse et al. 2012; Nettles et al. 2008).
The results of Molecular docking simulations determine a general binding mode of ligand.
RMSD value was calculated between the experimental binding mode of ligand rilpivirine as in X-ray co-crystallized pose in 3MEE and Glide re-docked pose to ensure accuracy and reliability of the docking procedure.
The binding mode of ligand analogues to an inward-facing conformation of the protein was investigated by X-ray crystallography.
Integrating the knowledge about the binding modes of ligands in different conformational states of the protein, separate pharmacophore models were generated and used for virtual screening to explore potential novel hits.
Mapping of benzene occupancy for trajectory structures with similar benzene binding modes at the pocket correlated well with previously seen interactors of the pocket, showing that our ligand-mapping simulations reproduce crystallographic binding modes of ligands on the PBD surface.
