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ModelZoo
RFDesign_rosetta
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a81d0061
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a81d0061
authored
Oct 21, 2023
by
zhuwenwen
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update readme
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README.md
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a81d0061
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@Author: zhuww
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@email: zhuww@sugon.com
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@Date: 2023-06-14 17:07:00
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@LastEditTime: 2023-10-2
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@LastEditTime: 2023-10-2
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# RFDESIGN
## 论文
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@@ -75,13 +75,14 @@ docker run -it --name rfdesign --shm-size=32G --device=/dev/kfd --device=/dev/d
运行hallucination或inpainting后,首先生成一个带侧链的松弛模型(.fas、.pdb、.npz、.trb 文件),该步骤需要.pdb和.npz文件,完成后,会生成一个FOLDER/trf_relax文件夹(包含松弛结构的pdb)
cd /opt/RFDesign/scripts
./trf_relax.sh FOLDER # FOLDER包含hallucination或inpainting的结果
./trf
old
_relax.sh FOLDER # FOLDER
文件夹
包含hallucination或inpainting的结果
#### AlphaFold2
根据hallucination设计模型和模板结构,进行AlphaFold2预测和计算RMSD:
./af2_metrics.py FOLDER/trf_relax # 修改第241行的data_dir为自己的alphafold2数据集路径
sh /opt/RFDesign/hallucination/models/alphafold/scripts/download_alphafold_params.sh alphafold-data # alphafold-data为下载模型的路径
./af2_metrics.py FOLDER/trf_relax # 修改第241行的data_dir为自己的alphafold2模型路径(即上一行的alphafold-data)
该步骤会将AF2模型输出到FOLDER/trf_relax/af2/,并将指标输出到FOLDER/af2_metrics.csv
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