Exploring the molecular surface

Stick models of the type shown in Plate 15a are the simplest and fastest type of model to compute and display because they represent the molecule with the smallest possible number of lines drawn on the screen. Stick models are relatively open, so the viewer can see through the outer regions of a complex molecule into the interior or into the interface between models of interacting molecules. But when the viewer wants to explore atomic contacts, a model of the molecular surface is indispensable. 

How then can you study the surface interactively The most common compromise is called a dotted surface (Plate 18), in which the program displays dots evenly spaced over the surface of the molecule. This image reveals the surface without obscuring the atoms within and can be redrawn rapidly as the viewer manipulates the model. Several types of surfaces can be computed, each with its own potential uses. One type is the van der Waals surface, in which all dots lie at the van der Waals radius from the nearest atom, the same as the surface of space-filling models. This represents the surface of contact between nonbonded atoms. Any model manipulations in which van der Waals 

Carrying out the same simulation that produces solvent-accessible surface displays, but locating the dots at the center of the probe molecule, produces the extended surface of the model. This display is useful for studying inter-molecular contacts. If the user brings two models together—one with extended surface displayed, the other as a simple stick model—the points of intermo-lecular contact are where the extended surface of one model touches the atom centers of the second model. 

Formulating proposed mechanisms of protein action requires investigating how proteins interact with ligands of all kinds, including other proteins. Molecular modeling programs allow the user to display and manipulate several 

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