Perspectives on Structural Molecular Biology Visualization: From Past to Present

Arthur J. Olson
2018 Journal of Molecular Biology  
Visualization has been a key technology in the progress of structural molecular biology for as long as the field has existed. This perspective describes the nature of the visualization process in structural studies, how it has evolved over the years, and its relationship to the changes in technology that have supported and driven it. It focuses on how technical advances have changed the way we look at and interact with molecular structure, and how structural biology has fostered and challenged
more » ... hat technology. Looking back on the development of what originally was termed "molecular graphics" we see a history of invention and innovation driven by a need to comprehend the complex nature of the molecular world. Graphics and visualization tools have been critical in enabling and catalyzing the remarkable progress of structural molecular biology from the past half century to today. Conversely over this time, the field of structural biology has helped to drive development and commercialization of computer graphics and visualization technologies. The Past Origins-Physical models were the earliest interactive three dimensional molecular visualization tools. Examples such as the CPK (Corey Pauling Koltun) 5 and Dreiding 6 models built upon earlier work going back to the mid-19 th century, when chemists such as Hoffmann and Kekule 2 built wooden ball-and-stick or wire models demonstrating element combining ratios or bond connectivity of simple chemical compounds. As X-ray crystallography began to produce three-dimensional molecular structures during the first half of last century, the need to represent them in accurate and comprehensible form increased the use of these physical models. In the 1950s they began to be used to model biological molecules. Pauling, who helped develop the CPK model and adopted the use of physical models throughout his career, used the simple process of folding a paper with a drawing of a polypeptide chain, coupled with his knowledge of the hydrogen bonding potential of amino acids to deduce the alpha helix as a folding motif for proteins 7 . Likewise, Watson and Crick, playing with brass models of nucleotide base structure, were able to explore geometric combinations to explain Franklin's fiber diffraction data and synthesize a model of the structure of DNA that revealed its genetic function. In a real sense both examples demonstrate how physical visualizations can promote exploratory interaction and serve as "analogue computers" leading to new insights 8;9 . Olson Highlights This perspective traces the evolution of structural molecular biology visualization from physical models of the earliest protein structures to immersive interaction of mesoscale models of cellular environments. Olson
doi:10.1016/j.jmb.2018.07.009 pmid:30009769 pmcid:PMC6186497 fatcat:4oxdbckyhbf6bh5dqgyfef4bra