Surface docking approaches

Figure 6.15 Description of the build-in and the surface docking approaches [60].

The groups of Wolfson and Nussinov have developed an approach for docking approach based on matching critical points [44-46]. These points define the knobs and holes on the two interacting surfaces. Both surface points and surface normals are matched and the approach can be implemented speedily. A global search takes of the order of minutes. After the search, putative solutions are checked to penalise overlap. In addition, the... 

LIGIN LIGIN uses a surface complementarity approach to dock rigid ligands into a rigid... 

In another definition, the term molecular surface has been introduced by Richards describing a molecular envelope accessible by a solvent molecule. These surfaces are used successfully in many chemical investigations, e.g., docking algorithms, free-energy surface density approaches, and visualization of molecular properties. ... 

To examine the effective interaction of urea with specific surfaces of KCl, an approach similar to surface docking developed to predict the influence of additives on the crystal morphology has been employed [21-27], The basis of this approach is to analyze the effect of additives on the individual crystal faces, which are cleaved from a crystal. If the additive has a preferred interaction on a special face, the growth of this face will be slower. As a result, the other fast-growing surfaces will disappear, and eventually, the slow-growing surface will control the morphology. In this way, the additive influences the morphology of crystals. For simulations of surfaces of crystalline solids, slab, and cluster models are nevertheless by far more popular because they are feasible from the computational point of view [28]. However, the cluster models came under scrutiny due to their finite size representation. Slab models rather mimic the infinite surface of solids and are considered to be a better approach than the cluster models. In this study, a conventional array of these alkali... 

The adsorption of the modifier-substrate complex onto Pt (111) surface was investigated using the Soiids-Docking module of the Insightll package. This module determines the conformations of the adsorbed molecules by a combined approach of high temperature molecular dynanuc simulations with molecular mechanics minimization. All the calculated structures were visualized on a Silicon Graphics workstation. 

Fig. 17. A space-fiUed CPK model of HO-1 showing the heme and His ligand. One propionate is quite exposed, as is one heme edge. This surface of the protein also is the most electropositive, which probably serves as the docking site for the electronegative P450 reductase. This would enable close approach of the FMN to heme for efficient electron transfer.

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