ASBT LB Analysis Scripts

Scripts used for analysis of MD simulation data of L. Biflexa ASBT (MD simulation files: https://osf.io/8rxzc/overview)

Scripts are archived in zenodo under the generic DOI https://doi.org/10.5281/zenodo.21224893

Script summaries:

• contacts.ipynb: calculates protein-DCA and lipid-DCA contact interactions given cutoff values

• contacts_plot.ipynb: Plots contact data generated by contacts.ipynb

• density.ipynb: Calculates density maps in .dx format

• domain_shifts.ipynb: Calculates and plots relative shifts in panel, core and membrane COMs

• prolif_fingerprint.ipynb: Calculates DCA ProLIF interaction fingerprint

• prolif_fingerprint_plot.ipynb: Plots interaction fingerprint data over repeats

Citation

Criska Li, Aurélien Grob, Leah Repa, Oliver Huxley, Deborah Brotherton, Patrick Becker, Ruby Dadzie, Oliver Beckstein, and Alexander Cameron. Structural insight into sodium-dependent bile acid transport by members of the SLC10 family. Structure (accepted)

preprint: bioRxiv https://doi.org/10.64898/2026.02.20.706973