Bringing Molecular Dynamics Simulation Data into View

Trends Biochem Sci. 2019 Nov;44(11):902-913. doi: 10.1016/j.tibs.2019.06.004. Epub 2019 Jul 10.


Molecular dynamics (MD) simulations monitor time-resolved motions of macromolecules. While visualization of MD trajectories allows an instant and intuitive understanding of dynamics and function, so far mainly static representations are provided in the published literature. Recent advances in browser technology may allow for the sharing of trajectories through interactive visualization on the web. We believe that providing intuitive and interactive visualization, along with related protocols and analysis data, promotes understanding, reliability, and reusability of MD simulations. Existing barriers for sharing MD simulations are discussed and emerging solutions are highlighted. We predict that interactive visualization of MD trajectories will quickly be adopted by researchers, research consortiums, journals, and funding agencies to gather and distribute results from MD simulations via the web.

Keywords: interactive visualization; molecular dynamics; molecular graphics; sharing; trajectory; web-based.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.
  • Review

MeSH terms

  • Computer Graphics
  • Macromolecular Substances / chemistry*
  • Molecular Conformation
  • Molecular Dynamics Simulation* / trends
  • Reproducibility of Results
  • Software
  • User-Computer Interface


  • Macromolecular Substances