PolarBearal 3.0

A highly accurate strand assignment and barrel analysis program.

Read our paper on cell.com | Install from source | Search the PolarBearal database

Introduction

This repository contains the algorithm, source code, and accompanying scripts for the latest version of PolarBearal3.

If you find our work useful, please consider citing our accompanying paper. Now published in Cell Press under the Biophysical Journal: https://doi.org/10.1016/j.bpj.2026.03.016.

Citation

Lim S, Nimmagadda T, Khamis A, Montezano D, Feehan R, Copeland M, Slusky JSG, Counting strands in outer membrane beta-barrels, Biophysical Journal (2026), doi: 10.1016/j.bpj.2026.03.016.

Installation

PolarBearal requires a C# runtime to build the executable.

• Windows/MacOS uses .NET 6.0 or higher.
• Build-compatible with Mono latest on Linux.

To install PolarBearal from source:

1. Clone the repository from Github.

git clone https://github.com/SluskyLab/PolarBearal3

2. Build the PolarBearal executable.

cd PolarBearal3 && dotnet build

Reproducing PolarBearal strand assignments from AlphaFoldDB

Note: PolarBearalDB strand number assignments are already available for public download as part of our IsItABarrel web application.

Download the AlphaFold structures necessary for barrel and strand counting analysis.

cd data/
chmod +x download_afdb_structures.sh
./download_afdb_structures.sh

After the structures have been downloaded, follow the menu to set your current dataset to the AlphaFold structures. The process has been automated through the example file commands.txt.

dotnet run < commands.txt

Given the large size of the dataset, we recommend running this as a detached or background process to avoid incomplete results.

Accessing predictions and results

Each PDB structure receives its own strand assignment and annotated PyMOL session. Batch results can be found under Output/....

License

PolarBearal is provided under the GPL 3.0 Public License. For more information, refer to our LICENSE file.