RiboDiffusion

Tertiary Structure-based RNA Inverse Folding with Generative Diffusion Models

Installation

Please refer to requirements.txt for the required packages.

Model checkpoint can be downloaded from here. Another checkpoint trained on the full dataset (with extra 0.1 Gaussian noise for coordinates) can be downloaded from here.

Download and put the checkpoint files in the ckpts folder.

Usage

Inference demo notebook to get started: <a target="_blank" href="https://colab.research.google.com/drive/199D6B0FsIYf-gW-hfMEBCcKaai_hM_cU"> <img src="https://colab.research.google.com/assets/colab-badge.svg" alt="Open In Colab"/></a>.

Run the following command to run the example for one sequence generation:

CUDA_VISIBLE_DEVICES=0 python main.py --PDB_file example/R1107.pdb

The generated sequence will be saved in exp_inf/fasta/R1107_0.fasta.

Multiple sequence generation can be run by:

CUDA_VISIBLE_DEVICES=0 python main.py --PDB_file example/R1107.pdb --config.eval.n_samples 10

For more sequence diversity, you can use exp_inf_large.pth or adjust the conditional scaling weight by --config.eval.cond_scale.

An example for adjusting the conditional scaling weight is as follows:

CUDA_VISIBLE_DEVICES=0 python main.py --PDB_file example/R1107.pdb --config.eval.n_samples 10 --config.eval.dynamic_threshold --config.eval.cond_scale 0.4

Citation

If you find this work useful, please cite:

@article{10.1093/bioinformatics/btae259,
    author = {Huang, Han and Lin, Ziqian and He, Dongchen and Hong, Liang and Li, Yu},
    title = {RiboDiffusion: tertiary structure-based RNA inverse folding with generative diffusion models},
    journal = {Bioinformatics},
    volume = {40},
    number = {Supplement_1},
    pages = {i347-i356},
    year = {2024},
    month = {06},
    issn = {1367-4811}
}

License

This project is licensed under the MIT License.