Biobox

Biobox is a Python package providing a toolbox for the manipulation, modelling and analysis of molecular structures.

AVAILABILITY

• Biobox is available on github.com/Degiacom-Lab/biobox
• The API is described at Degiacomi-Lab.github.io/biobox
• A Jupyter notebook presenting Biobox’s main functionalities is available at github.com/Degiacomi-Lab/biobox_notebook. The notebook can also be executed online (no need to install Python) on Binder.

APPLICATIONS

Biobox is at the backend of EMnIM , DynamXL and JabberDock. It has also been used to produce data featured in a range of publications, e.g.:

• Building polyhedral architectures in  I. Santhanagopalan et al., It takes a dimer to tango: Oligomeric small heat shock proteins dissociate to capture substrate, Journal of Biological Chemisty, 2018
• Creating super-coarse grain models in M.A. McDowell et al., Characterisation of ShigellaSpa33 and ThermotogaFliM/N reveals a new model for C-ring assembly in T3SS, Molecular Microbiology, 2016
• Analysing lipid density around a membrane protein in Landreh et al., Integrating mass spectrometry with MD simulations reveals the role of lipids in Na+/H+ antiporter, Nature Communications, 2017.

CITATION

If you use Biobox in your work, please cite:

Lucas S. P. Rudden, Samuel C. Musson, Justin L. P. Benesch, Matteo T. Degiacomi, Biobox: a toolbox for biomolecular modelling, Bioinformatics, 2021