Enlighten2: molecular dynamics simulations of protein-ligand systems made accessible.

Bioinformatics
Kirill Zinovjev, Marc W van der Kamp

Abstract

Experimental structural data can allow detailed insight into protein structure and protein-ligand interactions, which is crucial for many areas of bioscience, including drug design and enzyme engineering. Typically, however, little more than a static picture of protein-ligand interactions is obtained, whereas dynamical information is often required for deeper understanding and to assess the effect of mutations. Molecular dynamics (MD) simulations can provide such information, but setting up and running these simulations is not straightforward and requires expert knowledge. There is thus a need for a tool that makes protein-ligand simulation easily accessible to non-expert users. We present Enlighten2: efficient simulation protocols for protein-ligand systems alongside a user-friendly plugin to the popular visualization program PyMOL. With Enlighten2, non-expert users can straightforwardly run and visualize MD simulations on protein-ligand models of interest. There is no need to learn new programs and all underlying tools are free and open source. The Enlighten2 Python package and PyMOL plugin are free to use under the GPL3.0 licence and can be found at https://enlighten2.github.io. We also provide a lightweight Docker image via...Continue Reading

References

Apr 30, 2004·Journal of Computational Chemistry·Junmei WangDavid A Case
Jul 21, 2004·Journal of Computational Chemistry·Eric F PettersenThomas E Ferrin
Jul 12, 2011·Journal of Chemical Theory and Computation·Chresten R SøndergaardJan H Jensen
May 4, 2016·Journal of the American Chemical Society·Matthew J ByrnePaul R Race
May 25, 2016·Scientific Reports·João V RibeiroKlaus Schulten
Nov 1, 2017·Methods in Molecular Biology·Henrik Land, Maria Svedendahl Humble
Aug 20, 2019·Nature Communications·Kyle RiceGeoff P Horsman

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