Structure prediction techniques computational models

In Chapter 4, David Lewis introduces computer-assisted methods in the evaluation of chemical toxicology. He points out that any substance can be toxic, and thus it is the dose of the substance that determines a toxic response. How, then, does one predict toxicity Lewis examines QSAR methods, pattern recognition techniques, computer modeling, and knowledge-based systems to answer this question. Ideally, one would like to assess toxicity of a structure before the compound is synthesized. To bring all this into focus, emphasis is placed on the cytochromes P450. 

Other computer models and analytical tools are used to predict how materials, systems, or personnel respond when exposed to fire conditions. Hazard-specific calculations are more widely used in the petrochemical industry, particularly as they apply to structural analysis and exposures to personnel. Explosion and vapor cloud hazard modeling has been addressed in other CCPS Guidelines (CCPS, 1994). Again, levels of sophistication range from hand calculations using closed-form equations to numerical techniques. 

Here, we review how the development of SAXS as a structural technique is driven by advances in computer algorithms that allow to reconstruct low-resolution electron density maps ab initio from scattering profiles. In addition, we delineate how these low-resolution models can be used in free energy electrostatics calculations. Finally, we discuss how one can exploit the hierarchical nature of RNA folding by combining the low resolution, global information provided by SAXS with local information on RNA structure, from either experiments or state-of-the-art RNA structure prediction algorithms, to further increase the resolution and quality of models obtained from SAXS. 

The role of computer modelling in the science of complex solids including microporous materials was surveyed in Faraday Discussion 106 held in 1997. These techniques have now an increasingly predictive role. They can, for example, predict new microporous structures, design templates for their synthesis and model the static and dynamical behaviour of sorbed molecules within their pores,a topic of enduring importance and one of particular interest to Barrer. Computer modelling methods are, of course, most effective when used in a complementary manner with other physical techniques. Ref. 6 nicely illustrates this theme. Here EXAFS and quantum mechanical methods are used in a concerted manner to elucidate the structure of the active site in microporous titanosilicate catalysts. Articles in Faraday Discussions, vol. 106 again illustrate the complementarity of computational and experimental techniques. 

Hawley (64) first demonstrated the complex nature of moisture flow through wood above the fiber-saturation point resulting from capillary forces associated with air bubbles and pores of variable radii interconnecting cells. Using Comstock s (65) simplified structural model for softwoods, Spolek and Plumb (66), however, were able to predict the capillary pressures in southern yellow pine as a function of percent of water saturation of the cell cavities. Such a quantitative analysis would be more difficult to implement in the case of woods other than southern yellow pine because their structures and permeabilities are more variable in most cases. However, computer modeling techniques are developing to the point where more general models may become feasible. 

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