├── .gitignore ├── LICENSE ├── README.md ├── data ├── conditional_probs │ ├── ProteinMPNN │ │ └── .gitkeep │ └── raw_ProteinMPNN_outputs │ │ └── .gitkeep ├── constants.json ├── cv_folds_multiples_substitutions │ └── .gitkeep ├── cv_folds_singles_substitutions │ └── .gitkeep ├── embeddings │ ├── substitutions_multiples │ │ └── ESM2 │ │ │ └── .gitkeep │ └── substitutions_singles │ │ └── ESM2 │ │ └── .gitkeep ├── structures │ ├── coords │ │ └── .gitkeep │ └── pdbs │ │ └── .gitkeep └── zero_shot_fitness_predictions │ └── ESM2 │ └── 650M │ └── .gitkeep ├── environment.yml ├── example_scripts ├── conditional_probabilities_all.sh └── conditional_probabilities_single.sh ├── figures ├── calibration │ ├── calibration_metrics.png │ ├── error_based_ProteinNPT_summary.png │ ├── error_based_kermut_summary.png │ ├── kermut_domain_variance_summary_horizontal.png │ ├── rel_diag_ProteinNPT_summary.png │ ├── rel_diag_kermut_summary.png │ └── y_vs_y_pred │ │ ├── BLAT_ECOLX_Stiffler_2015_pred_vs_true_ProteinNPT.png │ │ ├── BLAT_ECOLX_Stiffler_2015_pred_vs_true_kermut.png │ │ ├── OPSD_HUMAN_Wan_2019_pred_vs_true_ProteinNPT.png │ │ ├── OPSD_HUMAN_Wan_2019_pred_vs_true_kermut.png │ │ ├── PA_I34A1_Wu_2015_pred_vs_true_ProteinNPT.png │ │ ├── PA_I34A1_Wu_2015_pred_vs_true_kermut.png │ │ ├── TCRG1_MOUSE_Tsuboyama_2023_1E0L_pred_vs_true_ProteinNPT.png │ │ └── TCRG1_MOUSE_Tsuboyama_2023_1E0L_pred_vs_true_kermut.png └── full_DMS │ ├── Spearman_comparison_plot_average_lower.png │ ├── Spearman_comparison_plot_average_upper.png │ ├── Spearman_comparison_plot_fold_contiguous_5_lower.png │ ├── Spearman_comparison_plot_fold_contiguous_5_upper.png │ ├── Spearman_comparison_plot_fold_modulo_5_lower.png │ ├── Spearman_comparison_plot_fold_modulo_5_upper.png │ ├── Spearman_comparison_plot_fold_random_5_lower.png │ └── Spearman_comparison_plot_fold_random_5_upper.png ├── kermut ├── __init__.py ├── calibration │ ├── __init__.py │ ├── _compute_confidence_interval_based_metrics.py │ └── _compute_error_based_metrics.py ├── cmdline │ ├── __init__.py │ ├── preprocess_data │ │ ├── __init__.py │ │ ├── extract_3d_coords.py │ │ ├── extract_ProteinMPNN_probs.py │ │ ├── extract_esm2_embeddings.py │ │ └── extract_esm2_zero_shots.py │ └── process_results │ │ ├── __init__.py │ │ ├── compute_calibration_metrics.py │ │ └── process_model_scores.py ├── constants │ ├── __init__.py │ ├── _alphabet.py │ ├── _colors.py │ └── _zero_shot_col.py ├── data │ ├── __init__.py │ ├── _filter.py │ ├── _prepare_GP_inputs.py │ ├── _prepare_GP_kwargs.py │ ├── _split_inputs.py │ ├── _standardize.py │ └── _tokenizer.py ├── gp │ ├── __init__.py │ ├── _gp.py │ ├── _instantiate_gp.py │ ├── _optimize_gp.py │ └── _predict.py ├── hydra_configs │ ├── benchmark.yaml │ ├── data │ │ ├── embedding │ │ │ └── esm2.yaml │ │ └── paths.yaml │ ├── kernel │ │ ├── kermut.yaml │ │ ├── kermut_constant_mean.yaml │ │ ├── kermut_esmif1.yaml │ │ ├── kermut_eve.yaml │ │ ├── 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