Experimental binding affinities for the protein-ligand complexes were taken from the PDBBind Database [69].
The DNA binding affinities for the target dicationic bis-guanidines were assessed by ΔTm values.
The results suggest that OsSMF1 has specific binding affinities for the three motifs and that it functions in a wide variety of seed developmental processes.
Molecular dynamics (MD) simulations are performed using constraint polypeptides that were combinatorially selected to have binding affinities for the noble metal platinum (Pt).
Preliminary biological evaluation of the analogue showed that a C10 hydroxymethyl substituent produced significant alterations in binding affinities for the ionotropic glutamate receptor subtypes.
The results were used to predict the binding affinities for the novel designed ZFs and may be used in engineering DNA binding proteins.
The results show that, compared with most scoring functions used in protein protein docking, MM/GBSA achieved better accuracy to predict the correct binding modes and binding affinities for the studied protein protein systems.
Previously, we have developed several vesamicol analogs with iodine into the 4-phenylpiperidine moiety as sigma receptor imaging agents and determined the binding affinities for the sigma receptors of the vesamicol analogs [21, 22].
The results of this study suggest that OsSMF1 is one of the key transcription factors that functions in a wide range of seed developmental processes with different specific binding affinities for the three DNA-binding motifs.
We also report significant variation in the pose and disparate binding affinities for the Gdm radicicol chimera radamide when bound to the two paralogs, which may be exploited in the design of paralog-specific inhibitors.
In addition, the molecular docking simulations revealed that compounds 6 with a flexible NHCOO show its binding affinities for the acetylcholine receptor (AChR), which may provide useful information for further design novel nematicides.
