Docking/modeling

Mizutani, M.Y., Tomioka, N., and Itai, A. Rational automatic search method for stable docking models of protein and ligand./. Mol. Biol. 1994, 243, 310-326. 

As can be seen in the contour map generated from the dock-aligned database, interaction with the hemin iron is a predominant component of the dock-minimized model. It follows that the predictivity of the 160 Dock model might favor compounds in which this interaction is influenced by the dock-minimization process. 

Analogue 422 is much less affected by the dock minimization and coincidentally is much less well predicted by the 160 Dock model. Though only 3% as active as artemisinin, this compound is predicted to be much more active than analogue 421. This added activity might be attributed to the focus by the dock model on the peroxide face interaction with hemin compounds with substituents on the (3-face are not as thoroughly represented by the model as a whole, and are less likely to be predicted well. 

M. Y. Mizutani, N. Tomioka, and A. Itai,/. Mol. Biol., 243, 310 (1994). Rational Automatic Search Method for Stable Docking Models of Protein and Ligand. 

Weber, C. H., and Vincenz, C. (2001). A docking model of key components of the DISC complex Death domain superfamily interactions redefined. FEES Lett. 492, 171-176. 

The same method has been applied to measure the Eli domain orientation when the protein is in complex with its RNA parmer or both RNA and thiostrepton antibiotic. The additional RDCs revealed a rearrangement of the N-terminal domain of Ell placing it closer to the RNA after binding of thiostrepton. HADDOCK has been used to calculate a model of the ternary stmcture of the Ell protein in complex with RNA and antibiotic. Based on the orientational data, the dynamics and the docking model, it seems that thiostrepton locks the domain conformation of Ell in a rigid (inhibitory) state. The antibiotic thiostrepton interferes with the interaction of elongation factors to this Ell-RNA region, which has a dramatic effect on the level of protein synthesis by the ribosome. 

Docking Models Based on Homology Modeling and Ligand Docking Methods. .. 287... 

Fig. 13 Docking models of an arylacetamide, the derivative of DuP 747 yellow), and a benzomorphan, MPCB (cyan), reported by Lavecchia et al. [36]. Reprinted from [36] with permission from American Chemical Society. Copyright (2000)...

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