├── .gitattributes ├── LICENSE ├── README.md └── code ├── DLKcat_comparison ├── .ipynb_checkpoints │ └── 02 - Predicting kcat values for a metabolic network-checkpoint.ipynb ├── 01 - Comparison of kcat predictions.ipynb └── 02 - Predicting kcat values for a metabolic network.ipynb ├── model_fitting ├── .ipynb_checkpoints │ ├── 01 Training xgboost models with enzyme and reaction information-checkpoint.ipynb │ ├── 02 - Testing additional input features-checkpoint.ipynb │ ├── 03 - Testing additional ML models-checkpoint.ipynb │ ├── 04 - Analyzing and plotting the results-checkpoint.ipynb │ └── 05 - Comparison to ENKIE-checkpoint.ipynb ├── 01 Training xgboost models with enzyme and reaction information.ipynb ├── 02 - Testing additional input features.ipynb ├── 03 - Testing additional ML models.ipynb ├── 04 - Analyzing and plotting the results.ipynb ├── CCB_plot_style_0v4.mplstyle ├── GNN_functions.py └── __pycache__ │ └── GNN_functions.cpython-37.pyc └── preprocessing ├── .ipynb_checkpoints ├── 01 - Data preprocessing-checkpoint.ipynb ├── 02 - Calculate reaction fingerprints and enzyme representations-checkpoint.ipynb ├── A1 - Data preprocessing-ESM1b_ts-checkpoint.ipynb ├── A1 - Data preprocessing-checkpoint.ipynb ├── A2 - Calculate reaction fingerprints and enzyme representations-ESM1b_ts-checkpoint.ipynb ├── A2 - Calculate reaction fingerprints and enzyme representations-checkpoint.ipynb ├── B1 - Creating input for reaction-GNN-checkpoint.ipynb ├── B2 - Calcuclating and mapping KM values-checkpoint.ipynb ├── Eukaryotes versus Prokaryotes-Copy1-checkpoint.ipynb ├── Eukaryotes versus Prokaryotes-Copy2-checkpoint.ipynb ├── Eukaryotes versus Prokaryotes-adding KM-checkpoint.ipynb └── Eukaryotes versus Prokaryotes-checkpoint.ipynb ├── 01 - Data preprocessing.ipynb ├── 02 - Calculate reaction fingerprints and enzyme representations.ipynb ├── CCB_plot_style_0v4.mplstyle ├── __pycache__ ├── GNN_functions_KM.cpython-36.pyc ├── GNN_functions_KM.cpython-37.pyc ├── data_preprocessing.cpython-37.pyc └── functions_and_dicts_data_preprocessing_GNN_KM.cpython-37.pyc ├── additional_input_features ├── .ipynb_checkpoints │ ├── 01 - Calcuclating and mapping KM values-checkpoint.ipynb │ ├── 02 - Mapping data points to BiGG reaction IDs-checkpoint.ipynb │ ├── 03 - Mapping fluxes to kcat values-checkpoint.ipynb │ ├── B2 - Calcuclating and mapping KM values-checkpoint.ipynb │ ├── B3 - Mapping data points to BiGG reaction IDs-Copy1-checkpoint.ipynb │ ├── B3 - Mapping data points to BiGG reaction IDs-checkpoint.ipynb │ └── B4 - Mapping fluxes to kcat values-checkpoint.ipynb ├── 01 - Calcuclating and mapping KM values.ipynb ├── 02 - Mapping data points to BiGG reaction IDs.ipynb ├── 03 - Mapping fluxes to kcat values.ipynb ├── BiGG_functions.py └── __pycache__ │ └── BiGG_functions.cpython-37.pyc └── data_preprocessing.py /.gitattributes: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AlexanderKroll/kcat_prediction/HEAD/.gitattributes -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AlexanderKroll/kcat_prediction/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AlexanderKroll/kcat_prediction/HEAD/README.md -------------------------------------------------------------------------------- /code/DLKcat_comparison/.ipynb_checkpoints/02 - Predicting kcat values for a metabolic network-checkpoint.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AlexanderKroll/kcat_prediction/HEAD/code/DLKcat_comparison/.ipynb_checkpoints/02 - Predicting kcat values for a metabolic network-checkpoint.ipynb -------------------------------------------------------------------------------- /code/DLKcat_comparison/01 - Comparison of kcat predictions.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AlexanderKroll/kcat_prediction/HEAD/code/DLKcat_comparison/01 - Comparison of kcat predictions.ipynb -------------------------------------------------------------------------------- /code/DLKcat_comparison/02 - Predicting kcat values for a metabolic network.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AlexanderKroll/kcat_prediction/HEAD/code/DLKcat_comparison/02 - Predicting kcat values for a metabolic network.ipynb -------------------------------------------------------------------------------- /code/model_fitting/.ipynb_checkpoints/01 Training xgboost models with enzyme and reaction information-checkpoint.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AlexanderKroll/kcat_prediction/HEAD/code/model_fitting/.ipynb_checkpoints/01 Training xgboost models with enzyme and reaction information-checkpoint.ipynb -------------------------------------------------------------------------------- /code/model_fitting/.ipynb_checkpoints/02 - Testing additional input features-checkpoint.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AlexanderKroll/kcat_prediction/HEAD/code/model_fitting/.ipynb_checkpoints/02 - Testing additional input features-checkpoint.ipynb -------------------------------------------------------------------------------- /code/model_fitting/.ipynb_checkpoints/03 - Testing additional ML models-checkpoint.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AlexanderKroll/kcat_prediction/HEAD/code/model_fitting/.ipynb_checkpoints/03 - Testing additional ML models-checkpoint.ipynb -------------------------------------------------------------------------------- /code/model_fitting/.ipynb_checkpoints/04 - Analyzing and plotting the results-checkpoint.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AlexanderKroll/kcat_prediction/HEAD/code/model_fitting/.ipynb_checkpoints/04 - Analyzing and plotting the results-checkpoint.ipynb -------------------------------------------------------------------------------- /code/model_fitting/.ipynb_checkpoints/05 - Comparison to ENKIE-checkpoint.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AlexanderKroll/kcat_prediction/HEAD/code/model_fitting/.ipynb_checkpoints/05 - Comparison to ENKIE-checkpoint.ipynb -------------------------------------------------------------------------------- /code/model_fitting/01 Training xgboost models with enzyme and reaction information.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AlexanderKroll/kcat_prediction/HEAD/code/model_fitting/01 Training xgboost models with enzyme and reaction information.ipynb -------------------------------------------------------------------------------- /code/model_fitting/02 - Testing additional input features.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AlexanderKroll/kcat_prediction/HEAD/code/model_fitting/02 - Testing additional input features.ipynb -------------------------------------------------------------------------------- /code/model_fitting/03 - Testing additional ML models.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AlexanderKroll/kcat_prediction/HEAD/code/model_fitting/03 - Testing additional ML models.ipynb -------------------------------------------------------------------------------- /code/model_fitting/04 - Analyzing and plotting the results.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AlexanderKroll/kcat_prediction/HEAD/code/model_fitting/04 - Analyzing and plotting the results.ipynb -------------------------------------------------------------------------------- /code/model_fitting/CCB_plot_style_0v4.mplstyle: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AlexanderKroll/kcat_prediction/HEAD/code/model_fitting/CCB_plot_style_0v4.mplstyle -------------------------------------------------------------------------------- /code/model_fitting/GNN_functions.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AlexanderKroll/kcat_prediction/HEAD/code/model_fitting/GNN_functions.py -------------------------------------------------------------------------------- /code/model_fitting/__pycache__/GNN_functions.cpython-37.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AlexanderKroll/kcat_prediction/HEAD/code/model_fitting/__pycache__/GNN_functions.cpython-37.pyc -------------------------------------------------------------------------------- /code/preprocessing/.ipynb_checkpoints/01 - Data preprocessing-checkpoint.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AlexanderKroll/kcat_prediction/HEAD/code/preprocessing/.ipynb_checkpoints/01 - Data preprocessing-checkpoint.ipynb -------------------------------------------------------------------------------- /code/preprocessing/.ipynb_checkpoints/02 - Calculate reaction fingerprints and enzyme representations-checkpoint.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AlexanderKroll/kcat_prediction/HEAD/code/preprocessing/.ipynb_checkpoints/02 - Calculate reaction fingerprints and enzyme representations-checkpoint.ipynb -------------------------------------------------------------------------------- /code/preprocessing/.ipynb_checkpoints/A1 - Data preprocessing-ESM1b_ts-checkpoint.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AlexanderKroll/kcat_prediction/HEAD/code/preprocessing/.ipynb_checkpoints/A1 - Data preprocessing-ESM1b_ts-checkpoint.ipynb -------------------------------------------------------------------------------- /code/preprocessing/.ipynb_checkpoints/A1 - Data preprocessing-checkpoint.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AlexanderKroll/kcat_prediction/HEAD/code/preprocessing/.ipynb_checkpoints/A1 - Data preprocessing-checkpoint.ipynb -------------------------------------------------------------------------------- /code/preprocessing/.ipynb_checkpoints/A2 - Calculate reaction fingerprints and enzyme representations-ESM1b_ts-checkpoint.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AlexanderKroll/kcat_prediction/HEAD/code/preprocessing/.ipynb_checkpoints/A2 - Calculate reaction fingerprints and enzyme representations-ESM1b_ts-checkpoint.ipynb -------------------------------------------------------------------------------- /code/preprocessing/.ipynb_checkpoints/A2 - Calculate reaction fingerprints and enzyme representations-checkpoint.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AlexanderKroll/kcat_prediction/HEAD/code/preprocessing/.ipynb_checkpoints/A2 - Calculate reaction fingerprints and enzyme representations-checkpoint.ipynb -------------------------------------------------------------------------------- /code/preprocessing/.ipynb_checkpoints/B1 - Creating input for reaction-GNN-checkpoint.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AlexanderKroll/kcat_prediction/HEAD/code/preprocessing/.ipynb_checkpoints/B1 - Creating input for reaction-GNN-checkpoint.ipynb -------------------------------------------------------------------------------- /code/preprocessing/.ipynb_checkpoints/B2 - Calcuclating and mapping KM values-checkpoint.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AlexanderKroll/kcat_prediction/HEAD/code/preprocessing/.ipynb_checkpoints/B2 - Calcuclating and mapping KM values-checkpoint.ipynb -------------------------------------------------------------------------------- /code/preprocessing/.ipynb_checkpoints/Eukaryotes versus Prokaryotes-Copy1-checkpoint.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AlexanderKroll/kcat_prediction/HEAD/code/preprocessing/.ipynb_checkpoints/Eukaryotes versus Prokaryotes-Copy1-checkpoint.ipynb -------------------------------------------------------------------------------- /code/preprocessing/.ipynb_checkpoints/Eukaryotes versus Prokaryotes-Copy2-checkpoint.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AlexanderKroll/kcat_prediction/HEAD/code/preprocessing/.ipynb_checkpoints/Eukaryotes versus Prokaryotes-Copy2-checkpoint.ipynb -------------------------------------------------------------------------------- /code/preprocessing/.ipynb_checkpoints/Eukaryotes versus Prokaryotes-adding KM-checkpoint.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AlexanderKroll/kcat_prediction/HEAD/code/preprocessing/.ipynb_checkpoints/Eukaryotes versus Prokaryotes-adding KM-checkpoint.ipynb -------------------------------------------------------------------------------- /code/preprocessing/.ipynb_checkpoints/Eukaryotes versus Prokaryotes-checkpoint.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AlexanderKroll/kcat_prediction/HEAD/code/preprocessing/.ipynb_checkpoints/Eukaryotes versus Prokaryotes-checkpoint.ipynb -------------------------------------------------------------------------------- /code/preprocessing/01 - Data preprocessing.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AlexanderKroll/kcat_prediction/HEAD/code/preprocessing/01 - Data preprocessing.ipynb -------------------------------------------------------------------------------- /code/preprocessing/02 - Calculate reaction fingerprints and enzyme representations.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AlexanderKroll/kcat_prediction/HEAD/code/preprocessing/02 - Calculate reaction fingerprints and enzyme representations.ipynb -------------------------------------------------------------------------------- /code/preprocessing/CCB_plot_style_0v4.mplstyle: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AlexanderKroll/kcat_prediction/HEAD/code/preprocessing/CCB_plot_style_0v4.mplstyle -------------------------------------------------------------------------------- /code/preprocessing/__pycache__/GNN_functions_KM.cpython-36.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AlexanderKroll/kcat_prediction/HEAD/code/preprocessing/__pycache__/GNN_functions_KM.cpython-36.pyc -------------------------------------------------------------------------------- /code/preprocessing/__pycache__/GNN_functions_KM.cpython-37.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AlexanderKroll/kcat_prediction/HEAD/code/preprocessing/__pycache__/GNN_functions_KM.cpython-37.pyc -------------------------------------------------------------------------------- /code/preprocessing/__pycache__/data_preprocessing.cpython-37.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AlexanderKroll/kcat_prediction/HEAD/code/preprocessing/__pycache__/data_preprocessing.cpython-37.pyc -------------------------------------------------------------------------------- /code/preprocessing/__pycache__/functions_and_dicts_data_preprocessing_GNN_KM.cpython-37.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AlexanderKroll/kcat_prediction/HEAD/code/preprocessing/__pycache__/functions_and_dicts_data_preprocessing_GNN_KM.cpython-37.pyc -------------------------------------------------------------------------------- /code/preprocessing/additional_input_features/.ipynb_checkpoints/01 - Calcuclating and mapping KM values-checkpoint.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AlexanderKroll/kcat_prediction/HEAD/code/preprocessing/additional_input_features/.ipynb_checkpoints/01 - Calcuclating and mapping KM values-checkpoint.ipynb -------------------------------------------------------------------------------- /code/preprocessing/additional_input_features/.ipynb_checkpoints/02 - Mapping data points to BiGG reaction IDs-checkpoint.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AlexanderKroll/kcat_prediction/HEAD/code/preprocessing/additional_input_features/.ipynb_checkpoints/02 - Mapping data points to BiGG reaction IDs-checkpoint.ipynb -------------------------------------------------------------------------------- /code/preprocessing/additional_input_features/.ipynb_checkpoints/03 - Mapping fluxes to kcat values-checkpoint.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AlexanderKroll/kcat_prediction/HEAD/code/preprocessing/additional_input_features/.ipynb_checkpoints/03 - Mapping fluxes to kcat values-checkpoint.ipynb -------------------------------------------------------------------------------- /code/preprocessing/additional_input_features/.ipynb_checkpoints/B2 - Calcuclating and mapping KM values-checkpoint.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AlexanderKroll/kcat_prediction/HEAD/code/preprocessing/additional_input_features/.ipynb_checkpoints/B2 - Calcuclating and mapping KM values-checkpoint.ipynb -------------------------------------------------------------------------------- /code/preprocessing/additional_input_features/.ipynb_checkpoints/B3 - Mapping data points to BiGG reaction IDs-Copy1-checkpoint.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AlexanderKroll/kcat_prediction/HEAD/code/preprocessing/additional_input_features/.ipynb_checkpoints/B3 - Mapping data points to BiGG reaction IDs-Copy1-checkpoint.ipynb -------------------------------------------------------------------------------- /code/preprocessing/additional_input_features/.ipynb_checkpoints/B3 - Mapping data points to BiGG reaction IDs-checkpoint.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AlexanderKroll/kcat_prediction/HEAD/code/preprocessing/additional_input_features/.ipynb_checkpoints/B3 - Mapping data points to BiGG reaction IDs-checkpoint.ipynb -------------------------------------------------------------------------------- /code/preprocessing/additional_input_features/.ipynb_checkpoints/B4 - Mapping fluxes to kcat values-checkpoint.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AlexanderKroll/kcat_prediction/HEAD/code/preprocessing/additional_input_features/.ipynb_checkpoints/B4 - Mapping fluxes to kcat values-checkpoint.ipynb -------------------------------------------------------------------------------- /code/preprocessing/additional_input_features/01 - Calcuclating and mapping KM values.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AlexanderKroll/kcat_prediction/HEAD/code/preprocessing/additional_input_features/01 - Calcuclating and mapping KM values.ipynb -------------------------------------------------------------------------------- /code/preprocessing/additional_input_features/02 - Mapping data points to BiGG reaction IDs.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AlexanderKroll/kcat_prediction/HEAD/code/preprocessing/additional_input_features/02 - Mapping data points to BiGG reaction IDs.ipynb -------------------------------------------------------------------------------- /code/preprocessing/additional_input_features/03 - Mapping fluxes to kcat values.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AlexanderKroll/kcat_prediction/HEAD/code/preprocessing/additional_input_features/03 - Mapping fluxes to kcat values.ipynb -------------------------------------------------------------------------------- /code/preprocessing/additional_input_features/BiGG_functions.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AlexanderKroll/kcat_prediction/HEAD/code/preprocessing/additional_input_features/BiGG_functions.py -------------------------------------------------------------------------------- /code/preprocessing/additional_input_features/__pycache__/BiGG_functions.cpython-37.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AlexanderKroll/kcat_prediction/HEAD/code/preprocessing/additional_input_features/__pycache__/BiGG_functions.cpython-37.pyc -------------------------------------------------------------------------------- /code/preprocessing/data_preprocessing.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AlexanderKroll/kcat_prediction/HEAD/code/preprocessing/data_preprocessing.py --------------------------------------------------------------------------------