RFdiffusion

简介

RFdiffusion is an open source method for structure generation, with or without conditional information (a motif, target etc). It can perform a whole range of protein design challenges as we have outlined in the RFdiffusion paper.

Things Diffusion can do:

  • Motif Scaffolding

  • Unconditional protein generation

  • Symmetric unconditional generation (cyclic, dihedral and tetrahedral symmetries currently implemented, more coming!)

  • Symmetric motif scaffolding

  • Binder design

  • Design diversification ("partial diffusion", sampling around a design)

安装步骤

1.克隆github仓库

git clone https://github.com/RosettaCommons/RFdiffusion.git

2.下载模型权重文件

cd RFdiffusion
mkdir models && cd models
wget http://files.ipd.uw.edu/pub/RFdiffusion/6f5902ac237024bdd0c176cb93063dc4/Base_ckpt.pt
wget http://files.ipd.uw.edu/pub/RFdiffusion/e29311f6f1bf1af907f9ef9f44b8328b/Complex_base_ckpt.pt
wget http://files.ipd.uw.edu/pub/RFdiffusion/60f09a193fb5e5ccdc4980417708dbab/Complex_Fold_base_ckpt.pt
wget http://files.ipd.uw.edu/pub/RFdiffusion/74f51cfb8b440f50d70878e05361d8f0/InpaintSeq_ckpt.pt
wget http://files.ipd.uw.edu/pub/RFdiffusion/76d00716416567174cdb7ca96e208296/InpaintSeq_Fold_ckpt.pt
wget http://files.ipd.uw.edu/pub/RFdiffusion/5532d2e1f3a4738decd58b19d633b3c3/ActiveSite_ckpt.pt
wget http://files.ipd.uw.edu/pub/RFdiffusion/12fc204edeae5b57713c5ad7dcb97d39/Base_epoch8_ckpt.pt

Optional:
wget http://files.ipd.uw.edu/pub/RFdiffusion/f572d396fae9206628714fb2ce00f72e/Complex_beta_ckpt.pt

# original structure prediction weights
wget http://files.ipd.uw.edu/pub/RFdiffusion/1befcb9b28e2f778f53d47f18b7597fa/RF_structure_prediction_weights.pt1

3.在conda中安装软件

srun -n 1 -p a100 --gres=gpu:1 --pty /bin/bash
module load miniconda3
module load gcc

conda env create -f env/SE3nv.yml

conda activate SE3nv
cd env/SE3Transformer
pip install --no-cache-dir -r requirements.txt
python setup.py install
cd ../.. # change into the root directory of the repository
pip install -e . # install the rfdiffusion module from the root of the repository

软件使用

测试软件是否能够正常使用

srun -n 1 -p a100 --gres=gpu:1 --pty /bin/bash
module load miniconda3
module load gcc

source activate SE3nv
./scripts/run_inference.py 'contigmap.contigs=[150-150]' inference.output_prefix=test_outputs/test inference.num_designs=10

如果能够正常在主屏幕输出且无报错，则软件可用。 更多参数和使用方式参见官网： https://github.com/RosettaCommons/RFdiffusion

最后更新: 2024 年 11 月 19 日