Molecular modeling computer graphics displays

Figure 8. Model of the dopamine receptor, with the (- -)-isobutactamol molecule superimposed, generated by the MMS-X computer-based molecular modeling and graphic display system. (Courtesy of Dr. G. Marshall, Washington University, St. Louis).

As the graphical capabilities of the computer systems became more powerful simultaneously the number of visualized structures increased. With the introduction of raster graphics (1974) and colored raster graphics displays (1979), other forms of molecular representations were possible [197]. CPK models could be represented and colored bonds or molecular surfaces could be visualized. 

The use of graphic displays as an essential element of computer-based instmctional systems has been exploited in a number of ways. Molecular modeling and visualization techniques have supplemented the traditional set of stick models in courses on organic and inorganic chemistry, and animation of molecular motion and of the progress or mechanism of chemical reactions has been a useful classroom tool. 

For new or would-be users of models, I present in Chapter 11 an introduction to molecular modeling, demonstrating how modern graphics programs allow users to display and manipulate models and to perform powerful structure analysis, even on desktop computers. This chapter also provides information on how to use the World Wide Web to obtain graphics programs and learn how to use them. It also provides an introduction to the Protein Data Bank (PDB), a World Wide Web resource from which you can obtain most of the available macromolecular models. 

Figure 5.1 Examples of some of the formats used by graphics packages to display molecular models on computer screens...

The 3D space requirements of most molecules can be represented to a good approximation by such Van der Waals surfaces. Fused sphere VDWS s are used extensively in molecular modeling, especially in the interpretation of biochemical processes and computer aided drug design. These approximate molecular surfaces are conceptually simple, their computation and graphical display on a computer screen take relatively short time, even for large biomolecules. 

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