Graphics display molecular surfaces

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. 

Grids of target-probe interaction energy values can be read into many molecular graphics programs which can display the MIFs as isoenergy contours or project the energies onto molecular surfaces. 

Tel. 619-534-5100, e-mail ccms-request sdsc.edu, dem scripps.edu Complete package for solving X-ray crystal structures such as those of proteins. SHAPE for analyzing molecular surfaces. FLEX for displaying and animating molecular graphics. Sun, Silicon Graphics, and DEC (ULTRIX) workstations. 

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. 

Connolly (43,44) and Richmond (45) also developed analytical methods for calculating molecular surface area and volume, which provide nearly exact values for the surface area and enclosed volume. Richmond s method provides analytical derivatives for surface area with respect to the cartesian coordinates of the atoms, which may be useful for docking (Section V). Connolly s algorithm also produces spectacular shaded raster graphics images (46), which give a very different feel for a macromolecular surface than conventional space-filling displays. 

The mid-range workstations offer 10 to 15 MIPS performance, with numeric processing at 1 to 2 MFLOPS, drawing rates of 200,000 to 400,0(X) v/s and 20,000 p/s. Their higher performance arises from so-call RISC architecture (Reduced Instruction Set CPU), which allow the computer to perform fewer tasks per CPU instruction. They also utilize faster, proprietary graphics display processors and larger display memory, which allows more colors and multiple windows. These units cost between 30,000 and 70,000, and they probably make up the bulk of recent CAMD woikstation purchases. They are suitable for solid model display and manipulation of small molecules, and wireframe and dot-surface display of macromolecules. Molecular mechanics and dynamics calcinations on small molecules and ensembles can be run in batch mode on these machines, and the results can be displayed and manipulated interactively. 

Cavity surfaces Earliest continuum models made use of oversimplified cavities for the insertion of the solute in the dielectric medium such as spheres or ellipsoids. In the last decades, the concept of molecular surface as become more common. Thus, the surface has been used in microscopic models of solution. Linear relationships were also found between molecular surfaces and solvation free energies. Moreover, given that molecular surfaces can help us in the calculation of the interaction of a solute molecule with surroundings of solvent molecules, they are one of the main tools in understanding the solution processes and solvent effects on chemical systems. Another popular application is the generation of graphic displays. ... 

Each of these types of molecular surfaces is adequate for some applications. So, the van der Waals surface is widely used in graphic displays. However, for the representation of... 

Of course, molecules are similar only if their chemical properties projected to some surface are similar. The most familiar molecular graphics display of properties is that of the molecular electrostatic potential as color-coded dots at the molecular surface. Figure 10 shows a black and white coding of electrostatic potential of the molecules in Figure 2. More recently, display of lipophilicity potentials at the van der Waals surface has been shown. ... 

An essay on the structural representation of sucrose has been published. Following an historical account of the establishment of the constitutional formula and confoimational features of sucrose, the present possibilities for graphics displays of its molecular geometry, contact surfaces, and hydrophobicity potential are given. ... 

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