McGibbon, R.T. et al. Biophys. J. 109, 1528–1532 (2015).

Molecular dynamics (MD) simulations are a powerful way to study protein structure and dynamics in silico. As more biologists become interested in using MD simulations to supplement wet lab studies, there is a growing need for the development of broadly accessible tools for analyzing MD trajectories. McGibbon et al. present MDTraj: fast, lightweight, user-friendly Python-based software for analyzing MD simulations. MDTraj accepts trajectory data from a wide range of MD file formats and is interoperable with existing Python-based statistical analysis and visualization tools. MDTraj enables a number of different MD trajectory analyses, including root-mean-square deviation calculations, extraction of order parameters and secondary-structure assignments. It also includes an interactive three-dimensional-structure viewer.