In the 3D-QSAR studies, the molecule alignment and conformation determination are so important that they affect the success of a model. The flexible docking is used on determination of ‘active’ conformation and molecular alignment. The figure shows the binding mode of N-phenyl-4-pyrazolo[1,5-b]pyridazin-3-ylpyrimidin-2-amines series derivatives to GSK-3. From the figure, we can see all the inhibitors share common binding features. The strategy of combining conformations and alignment obtained from the AutoDock3.0.5 with the CoMFA and CoMSIA produces a natural and reasonable elucidation of activation from a 3D-QSAR calculation. For details, see Xiao et al., pages 47–54.
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