2 - Molecular Graphics and Modeling: Tools of the Trade

Abstract

This chapter focuses on the generic features of the hardware and software requirements for molecular graphics and modeling systems. The computer-based techniques of molecular graphics and modeling initially developed quite separately into two distinct scientific disciplines. The first was in the pharmaceutical industry, and the search for an understanding between structure and function in drug design. This has driven the development of a diverse set of techniques for receptor modeling, structure-activity relationships, molecular similarity, and 3D database handling. The second area of initial development came from the protein crystallographic community, which requires tools for fitting and optimization of molecular structure into experimental electron density maps, and the subsequent analysis of protein structure and function. Although the computing power at the present time may be limiting for some of the more ambitious calculations and database searches, it is sufficient to perform most of the routine molecular modeling tasks on a small workstation. There is a major constraint in the power of the graphics and the way in which the chemist interacts with the data and its representation. It is probable that for some time to come, the computational techniques will fall short of being able to predict conformation and properties for all but the simplest system. Therefore, as in many skilled professions, the most important component in a successful molecular modeling study will be the quality and experience of the scientist involved. The equipment and techniques described in this chapter merely form the tools with which such modeling tasks can be attempted.