├── .gitignore ├── LICENSE ├── README.md ├── amino_acid_ordering.txt ├── misc ├── citation.bib ├── symbol_name.large.png └── symbol_name.png ├── predict ├── README.md ├── models │ ├── amino_acid_ordering.txt │ └── hsm_pretrained │ │ ├── Kinase_TK.npz │ │ ├── PDZ.npz │ │ ├── PTB.npz │ │ ├── PTP.npz │ │ ├── SH2.npz │ │ ├── SH3.npz │ │ ├── WH1.npz │ │ ├── WW.npz │ │ └── model_formats.csv ├── predict_domains.py ├── predict_proteins.py └── utils │ ├── __init__.py │ ├── dpi_prediction.py │ ├── load_models.py │ ├── ppi_prediction.py │ └── timeout_error.py ├── publication_analysis ├── README.md ├── netphorest │ ├── README.md │ ├── driver.sh │ ├── map_domain_netphorest_model │ │ ├── Kinase_TK_netphorest_model.csv │ │ ├── PTB_netphorest_model.csv │ │ ├── PTP_netphorest_model.csv │ │ └── SH2_netphorest_model.csv │ ├── process_netphorest_predictions.py │ └── write_fasta.py ├── pepint │ ├── README.md │ ├── driver.sh │ ├── map_domain_pepint_model │ │ ├── PDZ_pepint_model.csv │ │ └── SH2_pepint_model.csv │ ├── process_pepint_predictions.py │ └── write_fasta.py ├── pssm │ ├── README.md │ ├── driver.sh │ ├── map_domain_raw_preprocessed │ │ ├── Kinase_TK_matched_domseqs.csv │ │ ├── PDZ_matched_domseqs.csv │ │ ├── PTB_matched_domseqs.csv │ │ ├── PTP_matched_domseqs.csv │ │ ├── SH2_matched_domseqs.csv │ │ ├── SH3_matched_domseqs.csv │ │ ├── WH1_matched_domseqs.csv │ │ └── WW_matched_domseqs.csv │ └── pssm.py └── results │ ├── Fig_2a_S3.ipynb │ ├── Fig_2b_Table_S5_inputs_Fig_3_S4_analysis_hsmp_proteome_predictions.ipynb │ ├── Fig_3_S4.nb │ ├── Fig_4_5_S5_S6.ipynb │ ├── Fig_6_S7.ipynb │ ├── README.md │ ├── Table_S3_pvals_delong.ipynb │ └── scripts │ ├── combine_fold_rocs.py │ ├── compare_auc_delong_xu.py │ ├── experimental_proportions.py │ └── utils.py └── train ├── Analyze_training.ipynb ├── README.md ├── convert_binding_data.py ├── models ├── __init__.py ├── constants.py ├── hsm_d.py ├── hsm_d_singledomain.py ├── hsm_id.py └── utils.py ├── output_models.py ├── train.py 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