├── .gitignore ├── Flexpert-Design ├── README.md ├── configs │ ├── ANMAwareFlexibilityProtTrans.yaml │ ├── Flexpert-Design-inference.yaml │ ├── ProteinMPNN.py │ └── ProteinMPNN.yaml ├── data_interface.py ├── data_utils.py ├── download-cath-data.sh ├── model_interface.py ├── predict.py ├── predict_example │ ├── 1ah7_A.pdb │ ├── 1ah7_A_instructions.csv │ ├── compare_seqs.py │ └── predictions.txt ├── requirements.txt ├── src │ ├── __init__.py │ ├── datasets │ │ ├── __init__.py │ │ ├── alphafold_dataset.py │ │ ├── atlas_dataset.py │ │ ├── casp_dataset.py │ │ ├── cath_dataset.py │ │ ├── dataloader.py │ │ ├── fast_dataloader.py │ │ ├── featurizer.py │ │ ├── flex_cath_dataset.py │ │ ├── foldswitchers_dataset.py │ │ ├── mpnn_dataset.py │ │ ├── pdb_inference.py │ │ ├── ts_dataset.py │ │ └── utils.py │ ├── interface │ │ ├── __init__.py │ │ ├── data_interface.py │ │ ├── model_interface.py │ │ └── pretrain_interface.py │ ├── models │ │ ├── E3PiFold_model.py │ │ ├── MemoryESM.py │ │ ├── MemoryESMIF.py │ │ ├── MemoryPiFold.py │ │ ├── MemoryTuning.py │ │ ├── PretrainESMIF_model.py │ │ ├── PretrainESM_model.py │ │ ├── PretrainPiFold_model.py │ │ ├── Tuning.py │ │ ├── __init__.py │ │ ├── alphadesign_model.py │ │ ├── anm_prottrans.py │ │ ├── configs │ │ │ ├── ANMAwareFlexibilityProtTrans.yaml │ │ │ ├── AlphaDesign.yaml │ │ │ ├── E3PiFold.yaml │ │ │ ├── ESMIF.yaml │ │ │ ├── FlexibilityProtTrans.yaml │ │ │ ├── GCA.yaml │ │ │ ├── GVP.yaml │ │ │ ├── GraphTrans.yaml │ │ │ ├── KWDesign.yaml │ │ │ ├── PiFold.yaml │ │ │ ├── ProteinMPNN.yaml │ │ │ └── StructGNN.yaml │ │ ├── esmif_model.py │ │ ├── gca_model.py │ │ ├── graphtrans_model.py │ │ ├── gvp_model.py │ │ ├── kwdesign_model.py │ │ ├── pifold_model.py │ │ ├── proteinmpnn_model.py │ │ ├── prottrans.py │ │ └── structgnn_model.py │ ├── modules │ │ ├── E3PiFold.py │ │ ├── __init__.py │ │ ├── alphadesign_module.py │ │ ├── esmif_module.py │ │ ├── gca_module.py │ │ ├── graphtrans_module.py │ │ ├── gvp_module.py │ │ ├── pifold_module.py │ │ ├── pifold_module_old.py │ │ └── proteinmpnn_module.py │ ├── tools │ │ ├── __init__.py │ │ ├── config_utils.py │ │ ├── design_utils.py │ │ ├── logger.py │ │ ├── main_utils.py │ │ ├── metrics.py │ │ ├── parser.py │ │ ├── sequence_sampler.py │ │ └── utils.py │ └── version.py ├── train.py ├── train │ └── results │ │ └── MSEloss_flex_cath_coeff_0.8 │ │ └── checkpoints │ │ └── last.ckpt └── vanilla_mpnn_weights │ └── best-epoch=99-recovery=0.485.ckpt ├── Flexpert_logo.png ├── LICENCE ├── README.md ├── configs ├── data_config.yaml ├── env_config.yaml ├── lora_config.yaml └── train_config.yaml ├── data ├── PDBs │ ├── 1a62_A.pdb │ ├── 1ab1_A.pdb │ ├── 1ah7_A.pdb │ ├── 1ail_A.pdb │ ├── 1aol_A.pdb │ ├── 1b25_D.pdb │ ├── 1b2s_E.pdb │ ├── 1b2s_F.pdb │ ├── 1b8d_K.pdb │ ├── 1bgf_A.pdb │ └── paths.pdb_list ├── atlas │ ├── 2022_06_13_ATLAS_info.tsv │ ├── 2022_06_13_ATLAS_pdb.txt │ ├── download_analyses.py │ └── precomputed_flexibility_profiles │ │ ├── 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