BindCraft Scoring

This script evaluates the parameters used for loss and filtering in the BindCraft paper.

Usage

1. Clone ProteinMPNN inside the functions folder:

   git clone https://github.com/dauparas/ProteinMPNN functions/ProteinMPNN

2. Set up the BindCraft Conda environment as described in the original repo.
3. Provide the following inputs:
   a. FASTA file
   b. AlphaFold3 (AF3) results in a directory (see example inputs). ⚠️ The binder chain_ID should be "B" ⚠️
   c. PDB file of the target without any bind
   See the input_example to see what are the inputs and the outputs :)

Output:

The script generates a CSV file containing all scoring parameters.

🚧 Work in progress! 🚧