AlphaFold3 Local Installation Compatability Patch for AlphaBridge

This is the fork of the original AlphaBridge directory containing several bash and python scripts enabling the usage of local AlphaFold3 output by making it match the format of AlphaFoldServer.

Installation and Output Files

Instructions for installation of AlphaBridge and the information about the output format can be found in original repository: https://github.com/PDB-REDO/AlphaBridge/tree/trunk

How to run the script

1. Place your AF3 output files in directory AF3input

2. Run the script

You can either provide the desired seed number (put 1 if AF3 was used with a single seed) or use "best" functionality in which case the program will check ranking_scores.csv to find the seed with the best ranking scores.

bash run.sh
Usage: run.sh <seed_number> | best

Cleanup Scripts

You can either use

bash cleanup.sh

Or:

bash cleanupAFS.sh

Cleanup.sh will purge all files in AF3input, AFSConv, and AlphaBridge_output. CleanupAFS.sh will not affect AF3input and will remove all files edited by the program instead.

DEMO EXAMPLE

bash run.sh best

The output will be saved in AlphaBridge_output directory.