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