Structural Bioinformatics, 2nd Edition

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MOLECULAR VISUALIZATION

Steven Bottomley and Erik Helmerhorst

INTRODUCTION

Visual images are powerful. Images can turn something that may be unseen, abstract, theoretical, or complex into something real and purposeful. Visual images are not just decorations. In a glance, they can add meaning to a message, help people learn, and provide insight that is not possible by looking at the raw data alone. Scientific visualization generates visual images from data generated by scientific experiment and theory. It aims to discover new knowledge by distilling mountains of data into something immediately useful. Traditionally, line graphs, two-dimensional (2D) plots, three-dimensional (3D) plots, mathematical models, physical models, specimens, photographs, drawings, movies, and symbols are used to visualize scientific data. The computer has now become a convenient, and powerful, tool not only for traditional scientific visualization, but also for more challenging visualization tasks involving computer graphics, animations, modeling, and simulations. The importance of computer visualization to science is showcased in annual ’Visualization Challenge’ competitions (Nesbit and Bradford, 2006) and IEEE Visualization Conferences (Table 9.1).

Molecular Visualization

Molecular visualization is a way of seeing the abstract and unseen atomic and molecular world. It uses graphics to study structure, properties, and functions of molecules (Breithaupt, 2006). Consequently, it is also called molecular ...