Macromolecular modeling

Zhang Y, Liu H, Yang W (2002) Ab initio QM/MM and free energy calculations of enzyme reactions. In Schlick T., Gan H. H., (ed) Methods for Macromolecular Modeling. Springer-Verlag Berlin, pp 332-354... 

In many ways, the molecular models that we have used as the basis for our CAMD studies describe coal structure very well. However, none of the models investigated thus far contains explicit three-dimensional covalent cross-links. Actualfy, the models we have studied are primarily constructed of long chains of one-dimensionally-linked clusters with a number of short side-chains. However, it has been established on the basis of solvent swelling studies (11.15.16) that bituminous coal is primarily made up from a three-dimensional network of clusters held together by covalent bonds and by an even higher density of hydrogen bonds. These macromolecular models of coal, which are less concerned with the molecular structure than with the ways that clusters are bonded to one another, provide a complementary way of describing coal structure. 

In this article the use of formula 3 will always refer to rotated Fischer projections. In any case, the formulas must represent a section of chain long enough to illustrate the structural features excluding, unless explicitly required, the terminal groups. This representation corresponds to the use of a macromolecular model with an infinite chain length. 

Getting a macromolecular model model building, refinement, and validation... 

Bhat, T. N. and Cohen, C. H. (1984). OMITMAP An electron density map suitable for the examination of errors in a macromolecular model. /. Appl. Cryst. 17, 244-248. 

Rhodes, G. Crystallography Made Crystal Clear A Guide for Users of Macromolecular Models, 3rd ed. Academic Press New York, 2006. 

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. 

As a user of macromolecular models, you are faced with judging whether each model really supports the insights it appears to offer. The principles presented in Chapter 7, on how to judge the quality of models, apply to models obtained from all types of diffraction experiments. But today s structural databases also contain a growing number of models obtained by methods other than diffraction. In the next chapter, I will describe the origin of the major types of non-diffraction models and provide some guidance on how to use them wisely. 

Models are not molecules observed. No matter how they are obtained, before we ask what they tell us, we must ask how well macromolecular models fit with other things we already know. A model is like any scientific theory it is useful only to the extent that it supports predictions that we can test by experiment. Our initial confidence in it is justified only to the extent that it fits what we already know. Our confidence can grow only if its predictions are verified. 

---