On the Use of 1D, 2D, and 3D Visualization for Molecular Graphics

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A 3D visualization for a molecule.

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Macromolecular structures have become easily accessible by means of large databases, for example the World Wide Protein Data Bank. Several years ago, existing data in this field of research was rare and demanded for specialists and experts which wasted a lot of time to explore the data. Today, various visualisation techniques, tools, and systems have been designed and developed to support biochemists, chemists, or molecular biologists at certain tasks such as analysing protein functions, exploring ligand-binding sites, or understanding RNA signal and message processing. The intent of this paper is to discuss how 1D, 2D, and 3D representations are typically employed to facilitate some of these tasks. We describe common tasks that involve molecular structures and illustrate how 1D, 2D, and 3D visualisations are currently being used to address these. We discuss the benefits and drawbacks of these concepts in the context of these tasks and propose methods to provide empirical evidence by means of user evaluations.

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