Notes

Please visit our new repositories for AbX at https://github.com/CarbonMatrixLab/AbX and CarbonNovo at https://github.com/CarbonMatrixLab/carbonnovo. This repository will continue to host the code for CarbonDesign.

CarbonDesign

Contact
Haicang Zhang (zhanghaicang@sjtu.edu.cn)

Contributions
H.Z. conceived the ideas and implemented the CarbonDesign model and algorithms. H.Z. and M.R. designed the experiments, and M.R. conducted the main experiments and analysis. M.R. wrote the manuscript. H.Z., D.B. and C.Y. revised the manuscript.

Citation
Accurate and robust protein sequence design with CarbonDesign. M. Ren, C. Yu, D. Bu, H. Zhang. Nature Machine Intelligence. 6, 536–547 (2024). https://doi.org/10.1038/s42256-024-00838-2

Installation

1. CarbonDesign relies on the ESM2 language model. You can install ESM2 using the following command: pip install fair-esm.
2. Install other required libraries by running bash install.sh.

Model weights

1. Download CarbonDesign model weights from https://carbondesign.s3.amazonaws.com/params.tar, and place them in the ./params directory.
2. Download the ESM2 model weights from https://dl.fbaipublicfiles.com/fair-esm/models/esm2_t33_650M_UR50D.pt and https://dl.fbaipublicfiles.com/fair-esm/regression/esm2_t33_650M_UR50D-contact-regression.pt, and place them in the ./params directory.

Usage
You are required to input the PDB file (--data_dir) of the protein backbone structures. CarbonDesign will subsequently output the designed protein sequence (--output_dir). Additionally, CarbonDesign supports the prediction of the side chain structures of the designed sequences (--save_sidechain).
Example,

python -u run_carbondesign.py --data_dir ./data/pdbs  --output_dir ./results  --name_idx ./data/pdbs/name.idx

Main arguments:
data_dir: input directory of pdb files
output_dir: output directory
name_idx: list of pdb ids whose pdb files have been put in the input directory