Repositories list

• Communications

  Public
  An archival repository for all *completed* communications produced by the Brannigan Lab - posters/presentations, grants, manuscripts, theses, etc.

  PostScript

  •0•1•0•0•Updated Aug 18, 2025Aug 18, 2025

• blobulator

  Public
  Blob-based analysis of protein sequences - available online at blobulator.branniganlab.org and as an open-source tool.

  Python

  •

  GNU General Public License v3.0

  •1•1•93•1•Updated Aug 15, 2025Aug 15, 2025

• safep

  Public
  Tools for Analyzing and Debugging (SA)FEP calculations. See also the SAFEP Tutorial: https://github.com/jhenin/SAFEP_tutorial/tree/main Documentation: https://safep-alchemy.readthedocs.io/en/latest/

  molecular-dynamics-simulationfree-energy-perturbationsafep

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •1•6•21•2•Updated Aug 11, 2025Aug 11, 2025

• density_threshold_affinity

  Public
  Scripts to Assist Density Threshold Affinity Analysis - a method for obtaining free energies of protein-lipid binding. Originally described in: https://pubs.aip.org/aip/jcp/article/154/18/185102/200265/Spontaneous-lipid-binding-to-the-nicotinic and subsequently refined in: https://doi.org/10.1016/bs.mie.2024.03.008

  Python

  •0•1•62•2•Updated Aug 1, 2025Aug 1, 2025

• BranniganLab.github.io

  Public
  Lab Website

  CSS

  •

  Other

  •0•0•0•0•Updated Jul 1, 2025Jul 1, 2025

• nougat

  Public
  Analysis of membrane height, thickness, and curvature

  Python

  •0•3•87•1•Updated May 29, 2025May 29, 2025

• ELIC-phospholipid-identification

  Public
  Data and Analyses related to "Open-channel structure of a pentameric ligand-gated ion channel reveals a mechanism of leaflet-specific phospholipid modulation". Nat Commun 13, 7017 (2022). https://doi.org/10.1038/s41467-022-34813-5

  Rich Text Format

  •

  Other

  •0•0•2•0•Updated Mar 22, 2025Mar 22, 2025

• densitymap

  Public
  This project has moved to: https://github.com/BranniganLab/density_threshold_affinity. VMD and python tools for calculating and plotting 2D lipid density maps.

  Tcl

  •1•2•1•0•Updated Mar 27, 2024Mar 27, 2024

• lipid-monte-carlo

  Public
  Monte Carlo simulation of the Brannigan&Brown flexible lipid model. This is C code that GB wrote primarily as a graduate student.

  C

  •0•0•0•0•Updated Jul 16, 2021Jul 16, 2021