Perspectives on Structural Molecular Biology Visualization: From Past to Present

Abstract

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 that technology.

iCn3D, a Web-based 3D Viewer for Sharing 1D/2D/3D Representations of Biomolecular Structures

“…The annotations in iCn3D could also be retrieved by other tools. In the future, iCn3D may adopt emerging 3D technologies such as virtual reality (Goddard, et al, 2018; Goddard, et al, 2018; Olson, 2018).…”

Analogies in 3D molecular visualisations: development of a cell biology animation ‘How cells move – a new interpretation of old data’

“…The main aim in creating a model figure is to communicate with clarity the key messages the author needs to convey to their audience. However, a 2D schematic can often fall short when conveying molecular/cellular interactions, localisation, and structures that are highly dynamic or mechanistically complex [2,3]. Furthermore, the rich narrative in a research manuscript can be easily lost due to oversimplification of concepts and/or the illustration being confined to a single figure [4,5].…”

“…Whilst physical models and 2D diagrams continue to be used widely, scientists are becoming more aware of using in silico visual representations of their laboratory data to enhance communication of their ideas and aid learning, particularly as computer graphics and software continue to evolve [3,5,6]. Embedding of 3D data viewers (for structural biology and microscopy) within online research articles is steadily increasing [7].…”

Visualizing protein structures — tools and trends

“…Molecular visualization [1] in particular is now broadly used in many contexts, with the purpose of illustration in the scientific literature or the aim to gain insight about primary research data. A broad interest in and need for these methods exists for many decades as described in [2]. A key challenge is to pass information from intrinsically three-dimensional objects onto a two-dimensional support such as a sheet of paper or more commonly computer displays.…”

“…For instance, a first generic application concerns the illustration of scientific publications and the scrutiny of hypotheses [7], as for example relating mutational data to structural representations [8]. A further level of application may involve a more in-depth visual analysis of macromolecular structures and their properties [2], possibly related to the (spatial) distribution of charges, electrostatic properties, pockets and surface complementarities [4,9,10]. An even more specialized usage may refer to depicting and analyzing data from theoretical chemistry [9], computational biology [10] and bioinformatics approaches [11].…”