Visualizing protein structures - tools and trends

Biochem Soc Trans. 2020 Apr 29;48(2):499-506. doi: 10.1042/BST20190621.


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.

Keywords: molecular graphics; protein visualization; software tools; virtual reality.

Publication types

  • Research Support, Non-U.S. Gov't
  • Review

MeSH terms

  • Computational Biology / instrumentation*
  • Computational Biology / methods
  • Computer Graphics
  • Internet
  • Protein Conformation*
  • Proteins / chemistry*
  • Software*
  • Systems Biology
  • Ubiquitin
  • User-Computer Interface
  • Virtual Reality


  • Proteins
  • Ubiquitin