Treatment of Long-Range Forces and Potential

Abstract

The overall scope of this book is the implementation and application of available theoretical and computational methods toward understanding the structure, dynamics, and function of biological molecules, namely proteins, nucleic acids, carbohydrates, and membranes. The large number of computational tools already available in computational chemistry preclude covering all topics, as Schleyer et al. are doing in The Encyclopedia of Computational Chemistry [23]. Instead, we have attempted to create a book that covers currently available theoretical methods applicable to biomolecular research along with the appropriate computational applications. We have designed it to focus on the area of biomolecular computations with emphasis on the special requirements associated with the treatment of macromolecules. Part I provides an introduction to the field of computational biochemistry and biophysics for nonspecialists, with the later chapters in Part I presenting more advanced techniques that will be of interest to both the nonspecialist and the more advanced reader. Part II presents approaches to extract information from computational studies for the interpretation of experimental data. Part III focuses on methods for modeling and designing molecules. Chapters 14 and 15 are devoted to the determination and modeling of protein structures based on limited available experimental information such as primary sequence. Chapter 16 discusses the recent developments in computer-aided drug designs. The algorithms presented in Part III will see expanding use as the fields of genomics and bioinformatics continue to evolve. The final section, Part IV, presents a collection of overviews of various state-of-the-art theoretical methods and applications in specific areas relevant to biomolecules: protein folding (Chapter 17), protein simulation (Chapter 18), chemical process in solution (Chapter 19), nucleic acids simulation (Chapter 20), and membrane simulation (Chapter 21). In combination, the book should serve as a useful reference for both theoreticians and experimentalists in all areas of biophysical and biochemical research. Its content represents progress made over the last decade in the area of computational biochemistry and biophysics. Books by Brooks et al. [24] and McCammon and Harvey [25] are recommended for an overview of earlier developments in the field. Although efforts have been made to include the most recent advances in the field along with the underlying fundamental concepts, it is to be expected that further advances will be made even as this book is being published. To help the reader keep abreast of these advances, we present a list of useful WWW sites in the Appendix.