├── .gitignore ├── LICENSE ├── README.md ├── asset └── benchmark.png ├── config ├── multi_task │ ├── BERT │ │ ├── aav_contact_BERT.yaml │ │ ├── aav_fold_BERT.yaml │ │ ├── aav_ss_BERT.yaml │ │ ├── beta_contact_BERT.yaml │ │ ├── beta_fold_BERT.yaml │ │ ├── beta_ss_BERT.yaml │ │ ├── bindingdb_contact_BERT.yaml │ │ ├── bindingdb_fold_BERT.yaml │ │ ├── bindingdb_ss_BERT.yaml │ │ ├── binloc_contact_BERT.yaml │ │ ├── binloc_fold_BERT.yaml │ │ ├── binloc_ss_BERT.yaml │ │ ├── contact_fold_BERT.yaml │ │ ├── contact_ss_BERT.yaml │ │ ├── fluorescence_contact_BERT.yaml │ │ ├── fluorescence_fold_BERT.yaml │ │ ├── fluorescence_ss_BERT.yaml │ │ ├── fold_contact_BERT.yaml │ │ ├── fold_ss_BERT.yaml │ │ ├── gb1_contact_BERT.yaml │ │ ├── gb1_fold_BERT.yaml │ │ ├── gb1_ss_BERT.yaml │ │ ├── human_contact_BERT.yaml │ │ ├── human_fold_BERT.yaml │ │ ├── human_ss_BERT.yaml │ │ ├── pdbbind_contact_BERT.yaml │ │ ├── pdbbind_fold_BERT.yaml │ │ ├── pdbbind_ss_BERT.yaml │ │ ├── ppi_affinity_contact_BERT.yaml │ │ ├── ppi_affinity_fold_BERT.yaml │ │ ├── ppi_affinity_ss_BERT.yaml │ │ ├── solubility_contact_BERT.yaml │ │ ├── solubility_fold_BERT.yaml │ │ ├── solubility_ss_BERT.yaml │ │ ├── ss_contact_BERT.yaml │ │ ├── ss_fold_BERT.yaml │ │ ├── stability_contact_BERT.yaml │ │ ├── stability_fold_BERT.yaml │ │ ├── stability_ss_BERT.yaml │ │ ├── subloc_contact_BERT.yaml │ │ ├── subloc_fold_BERT.yaml │ │ ├── subloc_ss_BERT.yaml │ │ ├── thermo_contact_BERT.yaml │ │ ├── thermo_fold_BERT.yaml │ │ ├── thermo_ss_BERT.yaml │ │ ├── yeast_contact_BERT.yaml │ │ ├── yeast_fold_BERT.yaml │ │ └── yeast_ss_BERT.yaml │ ├── CNN │ │ ├── aav_contact_CNN.yaml │ │ ├── aav_fold_CNN.yaml │ │ ├── aav_ss_CNN.yaml │ │ ├── beta_contact_CNN.yaml │ │ ├── beta_fold_CNN.yaml │ │ ├── beta_ss_CNN.yaml │ │ ├── bindingdb_contact_CNN.yaml │ │ ├── bindingdb_fold_CNN.yaml │ │ ├── bindingdb_ss_CNN.yaml │ │ ├── binloc_contact_CNN.yaml │ │ ├── binloc_fold_CNN.yaml │ │ ├── binloc_ss_CNN.yaml │ │ ├── contact_fold_CNN.yaml │ │ ├── contact_ss_CNN.yaml │ │ ├── fluorescence_contact_CNN.yaml │ │ ├── fluorescence_fold_CNN.yaml │ │ ├── fluorescence_ss_CNN.yaml │ │ ├── fold_contact_CNN.yaml │ │ ├── fold_ss_CNN.yaml │ │ ├── gb1_contact_CNN.yaml │ │ ├── gb1_fold_CNN.yaml │ │ ├── gb1_ss_CNN.yaml │ │ ├── human_contact_CNN.yaml │ │ ├── human_fold_CNN.yaml │ │ ├── human_ss_CNN.yaml │ │ ├── pdbbind_contact_CNN.yaml │ │ ├── pdbbind_fold_CNN.yaml │ │ ├── pdbbind_ss_CNN.yaml │ │ ├── ppi_affinity_contact_CNN.yaml │ │ ├── ppi_affinity_fold_CNN.yaml │ │ ├── ppi_affinity_ss_CNN.yaml │ │ ├── solubility_contact_CNN.yaml │ │ ├── solubility_fold_CNN.yaml │ │ ├── solubility_ss_CNN.yaml │ │ ├── ss_contact_CNN.yaml │ │ ├── ss_fold_CNN.yaml │ │ ├── stability_contact_CNN.yaml │ │ ├── stability_fold_CNN.yaml │ │ ├── stability_ss_CNN.yaml │ │ ├── subloc_contact_CNN.yaml │ │ ├── subloc_fold_CNN.yaml │ │ ├── subloc_ss_CNN.yaml │ │ ├── thermo_contact_CNN.yaml │ │ ├── thermo_fold_CNN.yaml │ │ ├── thermo_ss_CNN.yaml │ │ ├── yeast_contact_CNN.yaml │ │ ├── yeast_fold_CNN.yaml │ │ └── yeast_ss_CNN.yaml │ └── ESM │ │ ├── aav_contact_ESM.yaml │ │ ├── aav_fold_ESM.yaml │ │ ├── aav_ss_ESM.yaml │ │ ├── beta_contact_ESM.yaml │ │ ├── beta_fold_ESM.yaml │ │ ├── beta_ss_ESM.yaml │ │ ├── bindingdb_contact_ESM.yaml │ │ ├── bindingdb_fold_ESM.yaml │ │ ├── bindingdb_ss_ESM.yaml │ │ ├── binloc_contact_ESM.yaml │ │ ├── binloc_fold_ESM.yaml │ │ ├── binloc_ss_ESM.yaml │ │ ├── contact_fold_ESM.yaml │ │ ├── contact_ss_ESM.yaml │ │ ├── fluorescence_contact_ESM.yaml │ │ ├── fluorescence_fold_ESM.yaml │ │ ├── fluorescence_ss_ESM.yaml │ │ ├── fold_contact_ESM.yaml │ │ ├── fold_ss_ESM.yaml │ │ ├── gb1_contact_ESM.yaml │ │ ├── gb1_fold_ESM.yaml │ │ ├── gb1_ss_ESM.yaml │ │ ├── human_contact_ESM.yaml │ │ ├── human_fold_ESM.yaml │ │ ├── human_ss_ESM.yaml │ │ ├── pdbbind_contact_ESM.yaml │ │ ├── pdbbind_fold_ESM.yaml │ │ ├── pdbbind_ss_ESM.yaml │ │ ├── ppi_affinity_contact_ESM.yaml │ │ ├── ppi_affinity_fold_ESM.yaml │ │ ├── ppi_affinity_ss_ESM.yaml │ │ ├── solubility_contact_ESM.yaml │ │ ├── solubility_fold_ESM.yaml │ │ ├── solubility_ss_ESM.yaml │ │ ├── ss_contact_ESM.yaml │ │ ├── ss_fold_ESM.yaml │ │ ├── stability_contact_ESM.yaml │ │ ├── stability_fold_ESM.yaml │ │ ├── stability_ss_ESM.yaml │ │ ├── subloc_contact_ESM.yaml │ │ ├── subloc_fold_ESM.yaml │ │ ├── subloc_ss_ESM.yaml │ │ ├── thermo_contact_ESM.yaml │ │ ├── thermo_fold_ESM.yaml │ │ ├── thermo_ss_ESM.yaml │ │ ├── yeast_contact_ESM.yaml │ │ ├── yeast_fold_ESM.yaml │ │ └── yeast_ss_ESM.yaml └── single_task │ ├── BERT │ ├── aav_BERT.yaml │ ├── beta_BERT.yaml │ ├── bindingdb_BERT.yaml │ ├── binloc_BERT.yaml │ ├── contact_BERT.yaml │ ├── fluorescence_BERT.yaml │ ├── fold_BERT.yaml │ ├── gb1_BERT.yaml │ ├── human_BERT.yaml │ ├── pdbbind_BERT.yaml │ ├── ppi_affinity_BERT.yaml │ ├── solubility_BERT.yaml │ ├── ss_BERT.yaml │ ├── stability_BERT.yaml │ ├── subloc_BERT.yaml │ ├── thermo_BERT.yaml │ └── yeast_BERT.yaml │ ├── CNN │ ├── aav_CNN.yaml │ ├── beta_CNN.yaml │ ├── bindingdb_CNN.yaml │ ├── binloc_CNN.yaml │ ├── contact_CNN.yaml │ ├── fluorescence_CNN.yaml │ ├── fold_CNN.yaml │ ├── gb1_CNN.yaml │ ├── human_CNN.yaml │ ├── pdbbind_CNN.yaml │ ├── ppi_affinity_CNN.yaml │ ├── solubility_CNN.yaml │ ├── ss_CNN.yaml │ ├── stability_CNN.yaml │ ├── subloc_CNN.yaml │ ├── thermo_CNN.yaml │ └── yeast_CNN.yaml │ ├── DDE │ ├── aav_DDE.yaml │ ├── beta_DDE.yaml │ ├── binloc_DDE.yaml │ ├── fluorescence_DDE.yaml │ ├── fold_DDE.yaml │ ├── gb1_DDE.yaml │ ├── human_DDE.yaml │ ├── ppi_affinity_DDE.yaml │ ├── solubility_DDE.yaml │ ├── stability_DDE.yaml │ ├── subloc_DDE.yaml │ ├── thermo_DDE.yaml │ └── yeast_DDE.yaml │ ├── ESM │ ├── aav_ESM.yaml │ ├── aav_ESM_fix.yaml │ ├── beta_ESM.yaml │ ├── beta_ESM_fix.yaml │ ├── bindingdb_ESM.yaml │ ├── bindingdb_ESM_fix.yaml │ ├── binloc_ESM.yaml │ ├── binloc_ESM_fix.yaml │ ├── contact_ESM.yaml │ ├── contact_ESM_fix.yaml │ ├── fluorescence_ESM.yaml │ ├── fluorescence_ESM_fix.yaml │ ├── fold_ESM.yaml │ ├── fold_ESM_fix.yaml │ ├── gb1_ESM.yaml │ ├── gb1_ESM_fix.yaml │ ├── human_ESM.yaml │ ├── human_ESM_fix.yaml │ ├── pdbbind_ESM.yaml │ ├── pdbbind_ESM_fix.yaml │ ├── ppi_affinity_ESM.yaml │ ├── ppi_affinity_ESM_fix.yaml │ ├── solubility_ESM.yaml │ ├── solubility_ESM_fix.yaml │ ├── ss_ESM.yaml │ ├── ss_ESM_fix.yaml │ ├── stability_ESM.yaml │ ├── stability_ESM_fix.yaml │ ├── subloc_ESM.yaml │ ├── subloc_ESM_fix.yaml │ ├── thermo_ESM.yaml │ ├── thermo_ESM_fix.yaml │ ├── yeast_ESM.yaml │ └── yeast_ESM_fix.yaml │ ├── LSTM │ ├── aav_LSTM.yaml │ ├── beta_LSTM.yaml │ ├── bindingdb_LSTM.yaml │ ├── binloc_LSTM.yaml │ ├── contact_LSTM.yaml │ ├── fluorescence_LSTM.yaml │ ├── fold_LSTM.yaml │ ├── gb1_LSTM.yaml │ ├── human_LSTM.yaml │ ├── pdbbind_LSTM.yaml │ ├── ppi_affinity_LSTM.yaml │ ├── solubility_LSTM.yaml │ ├── ss_LSTM.yaml │ ├── stability_LSTM.yaml │ ├── subloc_LSTM.yaml │ ├── thermo_LSTM.yaml │ └── yeast_LSTM.yaml │ ├── Moran │ ├── aav_Moran.yaml │ ├── beta_Moran.yaml │ ├── binloc_Moran.yaml │ ├── fluorescence_Moran.yaml │ ├── fold_Moran.yaml │ ├── gb1_Moran.yaml │ ├── human_Moran.yaml │ ├── ppi_affinity_Moran.yaml │ ├── solubility_Moran.yaml │ ├── stability_Moran.yaml │ ├── subloc_Moran.yaml │ ├── thermo_Moran.yaml │ └── yeast_Moran.yaml │ ├── ProtBert │ ├── aav_ProtBert.yaml │ ├── aav_ProtBert_fix.yaml │ ├── beta_ProtBert.yaml │ ├── beta_ProtBert_fix.yaml │ ├── bindingdb_ProtBert.yaml │ ├── bindingdb_ProtBert_fix.yaml │ ├── binloc_ProtBert.yaml │ ├── binloc_ProtBert_fix.yaml │ ├── contact_ProtBert.yaml │ ├── contact_ProtBert_fix.yaml │ ├── fluorescence_ProtBert.yaml │ ├── fluorescence_ProtBert_fix.yaml │ ├── fold_ProtBert.yaml │ ├── fold_ProtBert_fix.yaml │ ├── gb1_ProtBert.yaml │ ├── gb1_ProtBert_fix.yaml │ ├── human_ProtBert.yaml │ ├── human_ProtBert_fix.yaml │ ├── pdbbind_ProtBert.yaml │ ├── pdbbind_ProtBert_fix.yaml │ ├── ppi_affinity_ProtBert.yaml │ ├── ppi_affinity_ProtBert_fix.yaml │ ├── solubility_ProtBert.yaml │ ├── solubility_ProtBert_fix.yaml │ ├── ss_ProtBert.yaml │ ├── ss_ProtBert_fix.yaml │ ├── stability_ProtBert.yaml │ ├── stability_ProtBert_fix.yaml │ ├── subloc_ProtBert.yaml │ ├── subloc_ProtBert_fix.yaml │ ├── thermo_ProtBert.yaml │ ├── thermo_ProtBert_fix.yaml │ ├── yeast_ProtBert.yaml │ └── yeast_ProtBert_fix.yaml │ └── ResNet │ ├── aav_ResNet.yaml │ ├── beta_ResNet.yaml │ ├── bindingdb_ResNet.yaml │ ├── binloc_ResNet.yaml │ ├── contact_ResNet.yaml │ ├── fluorescence_ResNet.yaml │ ├── fold_ResNet.yaml │ ├── gb1_ResNet.yaml │ ├── human_ResNet.yaml │ ├── pdbbind_ResNet.yaml │ ├── ppi_affinity_ResNet.yaml │ ├── solubility_ResNet.yaml │ ├── ss_ResNet.yaml │ ├── stability_ResNet.yaml │ ├── subloc_ResNet.yaml │ ├── thermo_ResNet.yaml │ └── yeast_ResNet.yaml ├── peer ├── __init__.py ├── engine.py ├── flip.py ├── protbert.py └── util.py ├── requirements.txt └── script ├── run_multi.py └── run_single.py /.gitignore: -------------------------------------------------------------------------------- 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