Molecular modelling docking

Molecular Modeling, Small Molecule Docking, and Computational Analysis... 

Figure 21.2 Conceptualized construction of an A-B subunit protein toxin (left). The B chain contains a binding region for docking onto cell surfaces, while the A chain contains a catalytic site that produces cytotoxic affects intracellularly. The two subunits are joined by a disulfide bond that is reductively cleaved at the cellular level to allow the A subunit to affect cell death. A molecular model of ricin is on the right.

Tyler-Cross, R., M. Sobel, L.E. McAdory, and R.B. Harris. 1996. Structure-function relations of antithrombin Ill-heparin interactions as assessed by biophysical and biological assays and molecular modeling of peptide-pentasaccharide-docked complexes. Arch Biochem Biophys 334 206-213. 

As part of a subsequent study concerning primarily second-site revertant yeast iso-l-cytochrome c variants, Hazzard et al. evaluated the effect of converting Lys-72 to an aspartyl residue by site-directed mutagenesis on the electron transfer kinetics of the cytochrome c-cytochrome c peroxidase complex [136]. Lys-72 was of interest for this purpose, because it is involved in the hypothetical model for the complex formed by these two proteins that was proposed by Poulos and Kraut on the basis of molecular graphics docking [106]. In these... 

The Guy open conformation model docked structure was minimized in vacuo followed by a 1-ns molecular dynamics simulation of the complex embedded in a phosphatidylethanolamine (POPE) lipid bilayer. Adjustments were made to the model, and simulations were repeated so that very little movement occurred during the hnal iterations. Similar methods were used to dock the two domains in transitional and resting states. However, these results are more tenuous as little experimental data is available. In particular, the position of the S4-S5 linker and its role in opening and closing the pore are uncertain. The supplemental movie accompanying reference 36 illustrates the open-to-close-to-open cycle resulting from the simulations. 

Academia has been rich in producing theoretical computational methodology that underpins molecular modeling. The following software arose from universities or private and publicly funded institutes AMBER [10], INSIGHT [11,12], CHARMM [13], SYBYL [14], GRID [15], DOCK [16] and HINT (Hydropathic INTeractions) [39]. All except AMBER were commercialized. 

During the past several years, a variety of crystal structures of histone lysine and arginine methyltransferase in complex with the cofactor analog SAH and/or in complex with peptide substrates have been reported [92]. However, no 3D structure of a complex between a histone methyltransferase (HMT) and an inhibitor has been reported so far. Due to the lack of experimental structures, a variety of molecular modeling and docking studies has been carried out for H MTs in order to understand the structural requirements for inhibitor binding. 

Wang, D.-F., Helquist, P., Wiech, N.L. and Wiest, O. (2005) Toward selective histone deacetylase inhihitor design homology modeling, docking studies, and molecular dynamics simulations of human class I histone deacetylases. Journal of Medicinal Chemistry, 48, 6936-6947. 

Docking studies are molecular modeling studies aiming at finding a proper fit between a ligand and its binding site (IUPAC). 

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