mpnn_af2

ProteinMPNN-AF2 pipeline

Basic pipeline for protein design with ProteinMPNN and AF2 (ColabFold). It saves results in output folder

Usage

1. ProteinMPNN

Before running the script, prepare input file/folder and setup the script parameters.

SBATCH 01_mpnn.sh <input_file (pdb file/ folder with pdbs)>

2. AF2 prediction (ColabFold)

Follow the 02_prep_af2_inputs.ipynb notebook to prepare the inputs for AF2 prediction. Make sure to specify all the neccessary parameters. For instance, for prediction without MSA add --msa-mode single_sequence flag.

To do:

• notebook that uses only target MSA (and not for de novo designed binder)

3. Basic analysis of predicted structures

Example of basic analysis in 03_analyze_results.ipynb notebook.

To do:

• organize the code for metric calculation