├── EPP-MB ├── Readme.md ├── finetuning_cold_protein.ipynb ├── finetuning_random.ipynb ├── test_cold_protein.csv ├── test_random.csv ├── train_cold_protein.csv ├── train_random.csv └── valid.csv ├── LICENSE ├── PU_EPP_environment.yml ├── attention_visualization.ipynb ├── data ├── .placeholder ├── PU-EPP_testdata.csv ├── U_m_P │ └── .placeholder ├── example2.csv ├── example3_test.csv ├── example3_train.csv ├── example_id2seq.json ├── example_test.csv └── example_train.csv ├── figures ├── Figs for deep learning │ ├── Fig 3 Fig S5 │ │ ├── Data │ │ │ ├── aucmax_nopu.csv │ │ │ ├── aucmax_pu.csv │ │ │ ├── aucmax_small_datasets.csv │ │ │ └── flipres.json │ │ ├── Fig 3 and S5.ipynb │ │ ├── Fig 3.png │ │ └── Fig S5.png │ ├── Fig 5 │ │ ├── Data │ │ │ ├── chem_att_mapping_attention.json │ │ │ ├── chem_att_mapping_random_values.npy │ │ │ └── venn.xlsx │ │ ├── Fig 5.ipynb │ │ ├── Fig 5.png │ │ ├── upsetplot_OTA.png │ │ └── upsetplot_ZEN.png │ ├── Fig S1 │ │ ├── Fig S1.ipynb │ │ └── figures │ │ │ ├── Fig_S1_box_muliti_moles.png │ │ │ ├── Fig_S1_box_muliti_moles_reactions.png │ │ │ ├── Fig_S1_box_ota.png │ │ │ ├── Fig_S1_molecular_level.png │ │ │ ├── Fig_S1_molecular_level_mulit_moles.png │ │ │ ├── Fig_S1_reaction_level.png │ │ │ └── Fig_S1_reaction_level_multi_moles.png │ ├── Fig S2 │ │ ├── Fig S2.ipynb │ │ ├── Fig_S2_enzymes2molecules.png │ │ └── Fig_S2_molecules2enzymes.png │ └── Fig S3 S4 │ │ ├── Data │ │ ├── quantile_auc_mitdata.json │ │ └── quantile_mitdata.json │ │ ├── S3 S4.ipynb │ │ ├── S3.png │ │ └── S4.png └── Figs for molecular simulations │ ├── OTA │ ├── Data │ │ ├── OTA_APO │ │ │ ├── Apo.rmsf │ │ │ └── Apocross-correlation.dat │ │ ├── S1P2 │ │ │ └── S1P2.rmsf │ │ ├── S1P4 │ │ │ ├── S1P4.rmsf │ │ │ ├── S1P4_per_residue_contribution.dat │ │ │ └── S1P4cross-correlation.dat │ │ ├── S1P5 │ │ │ └── S1P5.rmsf │ │ └── mmgbsa.dat │ └── OTA analysis Figs S8, S9, S11, and S12.ipynb │ └── ZEN │ ├── Data │ ├── S1P4 │ │ ├── S1P4.rmsf │ │ ├── S1P4_per_residue_contribution.dat │ │ └── S1P4cross-correlation.dat │ ├── S1P5 │ │ └── S1P5.rmsf │ ├── S3P1 │ │ └── S3P1.rmsf │ ├── ZEN_APO │ │ ├── Apo.rmsf │ │ └── Apocross-correlation.dat │ └── mmgbsa.dat │ └── ZEA analysis Figs S8, S9, S11, and S12.ipynb ├── finetuning.ipynb ├── model ├── model.py ├── model_funetuning │ └── .placeholder ├── model_pretrained │ ├── PU-EPP_pretrained.pt │ └── word2vec_pretrained.model └── model_save │ └── .placeholder ├── predict.ipynb ├── readme.md ├── results ├── .placeholder └── log │ ├── .placeholder │ └── funetuning_log │ └── .placeholder ├── test.ipynb ├── train.ipynb └── utils ├── Radam.py ├── __init__.py ├── attentionvis.py ├── builder.py ├── data_parser.py ├── lookahead.py ├── tools.py ├── utils.py └── word2vec.py /EPP-MB/Readme.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xinghd142857/PU-EPP/HEAD/EPP-MB/Readme.md -------------------------------------------------------------------------------- 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