Visualizing protein structures — tools and trends

Abstract

Molecular visualization is fundamental in the current scientific literature, textbooks and dissemination materials. It provides an essential support for presenting results, reasoning on and formulating hypotheses related to molecular structure. Tools for visual exploration of structural data have become easily accessible on a broad variety of platforms thanks to advanced software tools that render a great service to the scientific community. These tools are often developed across disciplines bridging computer science, biology and chemistry. This mini-review was written as a short and compact overview for scientists who need to visualize protein structures and want to make an informed decision which tool they should use. Here, we first describe a few ‘Swiss Army knives’ geared towards protein visualization for everyday use with an existing large user base, then focus on more specialized tools for peculiar needs that are not yet as broadly known. Our selection is by no means exhaustive, but reflects a diverse snapshot of scenarios that we consider informative for the reader. We end with an account of future trends and perspectives.

High-performance macromolecular data delivery and visualization for the web

“…For alternative surveys of tools for molecular visualization, we direct the reader to Martinez et al (2020) and Miao et al (2019).…”

Seeing the PDB

“…This type of guided image creation is designed to give users some of the freedom that is possible in hand-drawn images, providing tools that enforce known relative sizes and behaviors of molecules while allowing easy, interactive construction of diverse subcellular scenes comprised of these molecules. New ways of seeing molecules for the challenges of today The molecular graphics techniques in widespread use today--bond diagrams, ribbon diagrams, dot surfaces, and spacefilling representations--are highly effective for research, dissemination and education/outreach (43,(56)(57)(58)(59). However, the field of structural biology continues to expand, and the classic graphical metaphors are providing the seeds for further exploration and development.…”

Computational tools for drawing, building and displaying carbohydrates: a visual guide

“…A recently developed version of UnityMol has been implemented with the immersive Virtual Reality context using head-mounted displays [ 87 ]. It offers high-quality visual representations, ease of interactions with multiple molecular objects, powerful tools for visual manipulations, accompanied by the evaluation of intermolecular interactions.…”