├── .DS_Store ├── .idea ├── .gitignore ├── .name ├── inspectionProfiles │ └── profiles_settings.xml ├── misc.xml ├── modules.xml ├── protease-gcnn-pytorch.iml └── vcs.xml ├── README.md ├── __init__.py ├── __pycache__ ├── layers.cpython-37.pyc ├── models.cpython-37.pyc └── utils.cpython-37.pyc ├── analysis ├── BenchmarkMLTrainigAfterPGCN.ipynb ├── MetricCalculationAfterTrain.ipynb ├── PlotLogoPlotSeqIdentityDataSummary.ipynb ├── PlotSankeyBarplot_Mutation.ipynb ├── PostAnalysisCrossTrainTest.ipynb ├── TestIndexSelection.ipynb ├── node_edge_weight_analysis_Joey.ipynb └── suppl │ ├── Table-S1A-HCV_sequence_protease_label.xlsx │ ├── Table-S1B-TEV_sequence_protease_label.xlsx │ ├── Table-S2-MetricSummary_ML_PGCN_suppl.xlsx │ ├── Table-S4-node_edge_importance_binary.xlsx │ ├── Table-S5-TEV_Daivd_Liu_Mutation_Sites_Numbering.xlsx │ ├── Table-S8-Yeast-assay_PGCN_predicted_results_TEV_designs .xlsx │ └── Table-S9-CrossTestSummary.xlsx ├── bin ├── graph_generation.sh ├── ml_benchmark.sh ├── test.sh ├── train.sh └── variable_importance.sh ├── data └── .ipynb_checkpoints │ └── ind.None-checkpoint.pose_indices ├── design_protease.py ├── graph ├── __pycache__ │ └── protein_graph.cpython-38.pyc ├── classifications │ ├── .ipynb_checkpoints │ │ ├── HCV_A171T-checkpoint.txt │ │ ├── PDZ_class-checkpoint.txt │ │ └── tev_design_for_validation_dual_directions_cleavage-checkpoint.txt │ ├── 20220911_tev_design_successes_p1pA.txt │ ├── 20220922_tev_design_dual_directions_cleavage.txt │ ├── 20220925_tev_design_p3.txt │ ├── 2bof-ER-summarized_label_singlePDB.txt │ ├── 2yol-ER-summarized_label_singlePDB.txt │ ├── 5gj4-ER-summarized_label_singlePDB.txt │ ├── 5y4l-ER-summarized_label_singlePDB.txt │ ├── HCV.txt │ ├── HCV_A171T.txt │ ├── HCV_D183A.txt │ ├── HCV_R170K_A171T_D183A.txt │ ├── PDZ_class.txt │ ├── TEV.txt │ ├── TEV_David_Liu_mutants_sequences_labels_no_single_three_libraries_duplicates_used4structGen_05_10_2022.csv │ ├── TEV_WT_balanced.txt │ ├── TEV_WT_not_exclusive.txt │ ├── TEV_final_all_var_noDup.txt │ ├── dvdar_design.txt │ ├── oydv-ER-summarized_label_singlePDB.txt │ ├── pgcn_rbd_class_file.txt │ ├── pgcn_rbd_class_file_ternary.txt │ ├── protease_3c_designs.txt │ ├── protease_3c_designs_2bof.txt │ ├── protease_3c_designs_5y4l.txt │ ├── protease_3c_designs_oydv.txt │ ├── tev-ER-summarized_label_singlePDB.txt │ ├── tev_design_20220912.txt │ ├── tev_design_for_validation_dual_directions_cleavage.txt │ ├── tev_design_negpool.txt │ ├── tev_oydv_design_candidates.txt │ ├── tev_oydv_expt_library_best_decoys.txt │ └── tev_oydv_raw_designs.txt ├── crystal_structures │ ├── HCV.pdb │ └── TEV_QS.pdb └── protein_graph.py ├── helper ├── .ipynb_checkpoints │ ├── 2yol-ER-summarized_label-checkpoint.txt │ ├── 2yol-ER-summarized_label_singlePDB-checkpoint.txt │ ├── RAAVGRG-checkpoint.fasc │ ├── Untitled-checkpoint.ipynb │ ├── generate_class_singlePDB-checkpoint.py │ └── make_modeling_commands-checkpoint.py ├── BenchmarkMLTrainAfterPGCN.py ├── generate_class_singlePDB.py ├── make_modeling_commands.py └── text_to_slurm.py ├── model ├── findBestAcc.py ├── findBestAcc_from_log.py ├── importance.py ├── layers.py ├── models.py ├── outputs │ ├── HCV_A171T_model.pth │ ├── HCV_Combined_model.pth │ ├── HCV_D183A_model.pth │ ├── HCV_Triple_model.pth │ ├── HCV_WT_model.pth │ └── TEV_model.pth ├── test.py ├── train.py └── utils.py └── pipeline.png /.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nucleus2014/protease-gcnn-pytorch/HEAD/.DS_Store -------------------------------------------------------------------------------- /.idea/.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nucleus2014/protease-gcnn-pytorch/HEAD/.idea/.gitignore -------------------------------------------------------------------------------- /.idea/.name: -------------------------------------------------------------------------------- 1 | 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