├── .gitignore ├── README.md ├── ckpt └── ProtLGN.pt ├── data.py ├── data └── example │ └── DATASET │ ├── CAPSD_AAV2S_Sinai_substitutions_2021 │ ├── CAPSD.pdb │ ├── CAPSD_AAV2S_Sinai_substitutions_2021.1.tsv │ ├── CAPSD_AAV2S_Sinai_substitutions_2021.10.tsv │ ├── CAPSD_AAV2S_Sinai_substitutions_2021.11.tsv │ ├── CAPSD_AAV2S_Sinai_substitutions_2021.12.tsv │ ├── CAPSD_AAV2S_Sinai_substitutions_2021.13.tsv │ ├── CAPSD_AAV2S_Sinai_substitutions_2021.14.tsv │ ├── CAPSD_AAV2S_Sinai_substitutions_2021.15.tsv │ ├── CAPSD_AAV2S_Sinai_substitutions_2021.16.tsv │ ├── CAPSD_AAV2S_Sinai_substitutions_2021.17.tsv │ ├── CAPSD_AAV2S_Sinai_substitutions_2021.18.tsv │ ├── CAPSD_AAV2S_Sinai_substitutions_2021.19.tsv │ ├── CAPSD_AAV2S_Sinai_substitutions_2021.2.tsv │ ├── CAPSD_AAV2S_Sinai_substitutions_2021.20.tsv │ ├── CAPSD_AAV2S_Sinai_substitutions_2021.21.tsv │ ├── CAPSD_AAV2S_Sinai_substitutions_2021.22.tsv │ ├── CAPSD_AAV2S_Sinai_substitutions_2021.23.tsv │ ├── CAPSD_AAV2S_Sinai_substitutions_2021.24.tsv │ ├── CAPSD_AAV2S_Sinai_substitutions_2021.25.tsv │ ├── CAPSD_AAV2S_Sinai_substitutions_2021.26.tsv │ ├── CAPSD_AAV2S_Sinai_substitutions_2021.27.tsv │ ├── CAPSD_AAV2S_Sinai_substitutions_2021.28.tsv │ ├── CAPSD_AAV2S_Sinai_substitutions_2021.3.tsv │ ├── CAPSD_AAV2S_Sinai_substitutions_2021.4.tsv │ ├── CAPSD_AAV2S_Sinai_substitutions_2021.5.tsv │ ├── CAPSD_AAV2S_Sinai_substitutions_2021.6.tsv │ ├── CAPSD_AAV2S_Sinai_substitutions_2021.7.tsv │ ├── CAPSD_AAV2S_Sinai_substitutions_2021.8.tsv │ ├── CAPSD_AAV2S_Sinai_substitutions_2021.9.tsv │ ├── CAPSD_AAV2S_Sinai_substitutions_2021.a3m │ ├── CAPSD_AAV2S_Sinai_substitutions_2021.fasta │ ├── CAPSD_AAV2S_Sinai_substitutions_2021.pdb │ └── CAPSD_AAV2S_Sinai_substitutions_2021.tsv │ └── GCN4_YEAST_Staller_induction_2018 │ ├── GCN4.fasta │ ├── GCN4.pdb │ ├── GCN4_YEAST_Staller_induction_2018.1.tsv │ ├── GCN4_YEAST_Staller_induction_2018.10.tsv │ ├── GCN4_YEAST_Staller_induction_2018.11.tsv │ ├── GCN4_YEAST_Staller_induction_2018.12.tsv │ ├── GCN4_YEAST_Staller_induction_2018.13.tsv │ ├── GCN4_YEAST_Staller_induction_2018.14.tsv │ ├── GCN4_YEAST_Staller_induction_2018.15.tsv │ ├── GCN4_YEAST_Staller_induction_2018.16.tsv │ ├── GCN4_YEAST_Staller_induction_2018.17.tsv │ ├── GCN4_YEAST_Staller_induction_2018.2.tsv │ ├── GCN4_YEAST_Staller_induction_2018.20.tsv │ ├── GCN4_YEAST_Staller_induction_2018.22.tsv │ ├── GCN4_YEAST_Staller_induction_2018.23.tsv │ ├── GCN4_YEAST_Staller_induction_2018.24.tsv │ ├── GCN4_YEAST_Staller_induction_2018.26.tsv │ ├── GCN4_YEAST_Staller_induction_2018.29.tsv │ ├── GCN4_YEAST_Staller_induction_2018.3.tsv │ ├── GCN4_YEAST_Staller_induction_2018.31.tsv │ ├── GCN4_YEAST_Staller_induction_2018.32.tsv │ ├── GCN4_YEAST_Staller_induction_2018.33.tsv │ ├── GCN4_YEAST_Staller_induction_2018.34.tsv │ ├── GCN4_YEAST_Staller_induction_2018.35.tsv │ ├── GCN4_YEAST_Staller_induction_2018.36.tsv │ ├── GCN4_YEAST_Staller_induction_2018.37.tsv │ ├── GCN4_YEAST_Staller_induction_2018.38.tsv │ ├── GCN4_YEAST_Staller_induction_2018.39.tsv │ ├── GCN4_YEAST_Staller_induction_2018.4.tsv │ ├── GCN4_YEAST_Staller_induction_2018.40.tsv │ ├── GCN4_YEAST_Staller_induction_2018.41.tsv │ ├── GCN4_YEAST_Staller_induction_2018.42.tsv │ ├── GCN4_YEAST_Staller_induction_2018.43.tsv │ ├── GCN4_YEAST_Staller_induction_2018.44.tsv │ ├── GCN4_YEAST_Staller_induction_2018.5.tsv │ ├── GCN4_YEAST_Staller_induction_2018.6.tsv │ ├── GCN4_YEAST_Staller_induction_2018.7.tsv │ ├── GCN4_YEAST_Staller_induction_2018.8.tsv │ ├── GCN4_YEAST_Staller_induction_2018.9.tsv │ ├── GCN4_YEAST_Staller_induction_2018.fasta │ ├── GCN4_YEAST_Staller_induction_2018.pdb │ ├── GCN4_YEAST_Staller_induction_2018.tsv │ └── run_alphafold.sh ├── environment.yaml ├── img └── logo.png ├── loc_pretrain.py ├── model.py ├── mutant_predict.py ├── norm └── cath_k10_mean_attr.pt ├── pretrain.py ├── requirements.txt ├── script ├── build_cath_dataset.sh ├── build_loc_dataset.sh ├── build_mutant_dataset.sh ├── metrics.sh ├── mutant_predict.sh ├── run_loc_train.sh └── run_pretrain.sh └── src ├── .DS_Store ├── Dataset ├── dataset_utils.py ├── localization_dataset.py ├── mutant_dataset.py └── protein_dataset.py ├── Egnnconfig ├── egnn.yaml └── egnn_mutant.yaml ├── Module ├── .DS_Store └── egnn │ ├── .DS_Store │ ├── __init__.py │ ├── egnn_pytorch.py │ ├── egnn_pytorch_geometric.py │ ├── network.py │ └── utils.py ├── metrics.py └── utils ├── .DS_Store ├── data_utils.py ├── draw_utils.py ├── train_utils.py └── utils.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bzho3923/ProtLGN/HEAD/.gitignore -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bzho3923/ProtLGN/HEAD/README.md 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