Structure-based Alignments Within 3D QSAR

Constantino et al. used the combination of a docking-based alignment and 3D QSAR analysis to build a predictive model for 46 poly(ADP-ribose)polymer-ase (PARP) inhibitors [67]. Representative PARP inhibitors were docked into 

The ability to predict accurately the binding conformation of tacrine, deca-methonium, edrophonium and huperzine gave confidence that we could use our model to evaluate the binding conformation of aminopyridazine compounds (Fig. 11.1). 

Since the aminopyridazine derivatives have a comparable size to decametho-nium and it is likely that they interact in a similar way with the binding site, we took the protein structure from the AChE-decamethonium complex for further docking. 

In the next step, we focused on a possible correlation between the derived AutoDock scoring values and the YETI protein-ligand interaction energies and the observed biological data. In an attempt to correlate the scoring values and 

To get an impression of which parts of the AChE inhibitors are correlated with variation in activity, we analyzed the PLS coefficient plots (obtained by 

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