Introduction

Most of the work described in the preceding chapters has dealt with the development of theoretical methods for studying the dynamics of proteins and nucleic acids or with the application of these methods to characterize the general properties of such molecules. A number of research groups have also started to apply theoretical methods to show how dynamics are involved in the function of specific biological molecules. In the coming years, theoretical methods will assume increasing importance as tools for answering practical questions in biochemistry and pharmacology. These tools will be used in the systematic interpretation of experimental data and in the prediction of properties of molecules prior to the synthesis or experimental study of such molecules. Theoretical methods will also continue to be used to answer more fundamental questions concerning the dynamic nature of these molecules. This chapter describes some of the work that is underway along these lines, and some of the directions in which this work is likely to lead.

The strengths of the methods described in this book are a consequence of the fact that the models are so detailed – every atom can be treated, and the potential functions can represent all forms of interatomic interactions. At the same time, it is this very detailed representation that produces the most serious limitations on the methods. By today's standards, a 100 ps molecular dynamics simulation of a macromolecule with a molecular weight of 30000 in solution is computationally very expensive.